From what it sounds like, essentially what you're asking is to completely throw away most of the lore and story of Refuge which would have to be either removed or all rewritten just to get to Refuge quicker. The whole refuge storyline is very much integrated into the main quest both up to now and presumably even more so into the future. Removing that would break lore, quests, and nothing would make any sense.
I dont feel that its as open and shut as that.
True that it would be a lot of extra work for an overworked team but I don't think, as someone who loves lore of games in general, that it disrupts the established lore as much as people are making it out to seem.
Once the undercaverns part of the quest is completed (which I personally think should be a requirement and is not at all difficult), MQ factions have nothing to do with the story (as far as the player base is concerned). If Iksith 2.5 or 3.0 or 1.1.5b opens up an invasion involving the MQ factions I could totally see it but that is beyond the scope of the player base and beyond the expectation of the player base to be released any time soon. That being said even Shaina, the one who sends you on the fool's errand, abandons them as quickly as their usefulness dries up and another option appears. None of the HFb events involve MQ factions, none of the refuge quests involve factions, none of the Iksith quests involve factions at all. There is NO involvement of factions after that. They are a stepping stone *spoilers* to find out something doesn't work. Again, if factions were at all important to the lore of this game, which they are pretty clearly not, then 2 of the 3 factions would also have finished quests but they don't. As I understand how projects work for the Dev team, they never will be finished either. Outside of the MQ you have to go out of your way in the old world to find mentions of Kaezul beyond areas he fucked over. Even there they talk about the effect he has (plague) and not on the story that has developed. So to say it breaks lore is pretty weak tea.
There is no basis for actually understanding how the old world works. Its been 15 years in game since Newport's founding. Is that from the day they laid the first stone (them some real good contractors) or the day Newport looked like we as players see it? Its been 55 years in game since we started reclaiming the lands taken and ruined by Kaezul but we have to run around to find people who remember it (all from the MQ). A total of just over 150 years since his actual invasion. There is an elf that still remembers, are elves (like most fantasy games) significantly long lived? What is the average life expectancy of a human? Why is there an "ancient elven culture" that has greater magical knowledge than has been seen before, located in human lands, when Elves themselves are not so much older of a race than any of the young races? Why is Underhill, one of the last to fall to Kaezul and still struggling to feed its people, not at all worried about his return? How is it that 150 years has passed and someone who destroyed half of the known world and set the playable races back probably 300 years not still fresh on every NPCs lips? It destroyed the largest old world civilization in history, cause more than half of the dark elves turn on their own and left all they had known and loved tainted and scarred but no one loses sleep of his return?
If we are to assume the hero fantasy, the first time your character does anything is the first time its been done. Information would have trickled back through the raiding events that occur from time to time that the old world has gained in strength and there is an organized movement (seekers) actively defending its lands and that they have found ways to undo some of the damage that has been done (athica, kelethin). The refugees would absolutely be looking for high ranking contacts in this movement but by the end of the heartlands chain you are already tied with Gavin and presumably one of the very few who actually get to talk to Shaina. Not to mention falling back to hero fantasy, youre one of the first people from the old world to voluntarily step onto Iksith and go looking for an organization that is also looking for you. You cannot bring any force you have earned from MQ faction to bear. Any incursion from Blackscale or Silver Crown would be met with instant aggression or mist rendering them moot and any supplies from Silver Crown or CoI (again failing to feed their own people) would tip off the location of the refugees or risk falling into enemy hands again tipping them off to your arrival. No amount of cigars or gnomish sex robot fantasies you fulfill changes that outcome up to where the player base is able to reach.
Allowing new players access to runic spells or ports changes very little in the long run with balance but makes a large difference to new players and what they feel they can accomplish while playing with others. I am not suggesting that we allow new players to bypass MQ factions by any stretch or to award them augments but taking down some of the longer time sink barriers to this games interesting lore and class features might do well to keeping new player base. Removing or lowering the barrier does not decrease the amount of people in Iksith, it does not decrease the difficulty in the content. It might increase player satisfaction, it might encourage class diversity and it could increase player longevity. What feels better "Oh, its gonna rot. Loot it because you'll need it some day." or "Great, you got a piece for your Runic spell. That really rounds out the class."
I know personally, seeing that I had to get up to R1 or R2 on a beastlord to get the most out of the class was a turn off for me before I did any refuge quests. It is more of a turn off for me now that I have.
TL;DR: Lore excuse is weak tea. There is a lot of time invested to get access to all your class can do. Lowering the bar to entry but not the bar for rewards might help us as a server in the long run.