I dont keep really any money in any exchanges that i am not comfortable losing at any moment. But I am also not a day trader, so if I want to trade for something its like a 3 hour process for me. Put the money in, traade it for whatever, take the money out.
I leave about 1.5 BTC in coinbase for the various btc apps i use to pay for stuff but thats about it.
But to be honest, Bitstamp handled it very well and I wouldn't give up on them yet. These things happen in this space. The big companies become heavy targets and thats part of the risk of being a day trader (which is what keeping your money in these exchanges is really for, high frequency trading).