Keep in mind that caps also effect things like bases, cars, car modifications, keys, etc. As said before in another merc thread, if the problem is really that bad then all the devs have to do is switch merc prices from caps to something like faction points.
This way all the big gangs start clean with mutie/merc purchases while leaving bank interest for the little joes. As you said the smaller gangs don't or cannot afford to do TC merc battles anyways so why fuckup the bank interest system for them.