That sucks Monsterer, hopefully this motivates you to improve the back end of Metaexchange a little bit. Coin market cap uses the price of each exchange, weighted by how much volume they've had in the last 24 hours. I think perhaps you can improve upon that formula by using a combination of the median price and CMC's formula. Obviously you've thought of this but a killswitch would be good too, if the price moves X% you should freeze trading until you manually OK it.
I've been working on creating part of a Meteor app (javascript & node.js) that aggregates data from 31 exchanges... it is a pain in the ass because every exchange has a different format for everything whether it be the format of their JSON, or the denomination they show price or volume. It is incomplete, but I'd be happy to share my code with you if you want to build a custom solution and cut CMC out of the loop. I admit I haven't programmed anything in about 10 years though, so my code is rough around the edges so to speak. This project is just to reacquaint myself with programming for fun so I wouldn't mind sharing the code, although I do plan on building a site around the code I'm writing. I have 31 exchanges working and am looking to implement another ~40 more. I can understand why you're using CMC though... it is a PITA to integrate a lot of exchange's APIs.