As far as I can remember, the Imperial Cult and Thieves Guild quests don't intersect. Quests intersecting is the only factor in Morrowind when you have to fear that you cannot complete a guild. This happens between Thieves and Fighters Guild, at least. Otherwise, you can do any guilds wholly, even if they were each others' sworn enemies. Telvanni and Mages Guild is an example close to that. You can still become the head of both with one character.
So, yes, it's just a strange phase in Klawed's life, and it has no effect on his status in the Thieves Guild.
Minor Thieves Guild spoiler follows.
Spoiler Besides, you'll be doing a bit more charity in the late stages of Thieves Guild.
They're not all that evil themselves.
See? I was even kind enough to close to spoiler tag it even though this is a spoiler forum.