There are good arguments both for and against main tank gearing. If your guild chooses to give the MT priority on tanking loot, that's a reasonable decision. The question is, are you comfortable with the guild's loot system? If you are, stay. If you aren't, talk with the guild leadership about it. You may want to consider looking for another guild.
Personally, I'd be fine with the MT getting loot priority if there were a formal system like DKP where the MT was allowed to spend into the negative so they could get loot first. I'd be comfortable with that because I knew I'd eventually be able to catch up. I wouldn't be comfortable with MT gearing in a loot council system because I wouldn't have a built-in guarantee that I'd eventually get my fair share of loot.
That's just me, though. What matters is your feelings. What is it about the idea that makes you uncomfortable. Are you not confident that the guild will progress and that you will eventually get loot? Are you worried that the MT will leave the guild, putting all that gear the guild gave him to waste?
Also, how long have both you and the MT been with the guild?
"The best way out is always through." —Robert Frost