| Well, what's very strange, the only conflicting loyalty i've met is between Fighters and Thieves Guilds (code book). As soon i'm not going to make a career in any of them, it doesn't hinder me in any way. My char. is head of Redorans, Temple, Cult and Mages Guild and just haven't had a leisure to throw down the gauntlet to claim the leadership of Legion in Morrowind (although having rights and matching requiremens). So far no conflicts of any kind. Yes, there was a confrontation - with Buoyant Armigers, but it was a matter of courtesy and resolved in poetry riddle contest and never spoiled the attitude of Temple and Ordinators to my protagonist (BTW, was the quest mentioned above really to kill? Would you, please, see your journal once more?)...
My guess is one may get different quests depending on reputation or personality (or both) and other attributes maybe. I joined the Legion late enough with rep. about or over 30 (have never had a bounty on my character's head). It's also quite possible the class has some impact (my hero is a Withchunter).
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Loredweller
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...for tomorrow never comes ...
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