The 3 levels it so you may gain from the MSQ for post-ARR level 50 quests is but a drop in the bucket. I’d say just do them anyway.
Everyone playing at the time did. We all got into Ishgard at level 50. It won’t really ruin the experience or hold you back.
Alternatively if this one s still an issue for you, try levelling another job, or work on pvp, or mgp, or the other myriad things of objectives the game has for us to enjoy.