Try to see if you can find trip curves for the breakers and fuses you will be using. Fuses and circuit breakers don't conduct at 89.9A and then turn off instantly at 90A. Every protection element has a current vs. time curve that tells you how long it will take to break the circuit for a given overcurrent condition. This is where "slow-blow", "fast-acting", etc terminology comes from. TPA previously mentioned QO-series breakers from Square D. Here is a link to their document with the trip curve on page 20:
http://ecatalog.squared.com/pubs/Circui ... 01R108.pdf
At rated current, the breaker will take upwards of 10 minutes to trip. At 2x rated, it will trip in about 10 seconds. At 10x rated, it will trip in milliseconds. Fuses operate on thermal principles (melting the strip), but circuit breakers usually have both thermal (bimetallic strip) and magnetic/inductive mechanisms. For the thermal-triggered regions, you get a curve with an I^2*T shape, based on how much energy it takes to heat up the strip to trigger temperature. Some manufacturers rate their fuses in terms of I^2*T. Different parts will have different curves, but the basic shape is the same.
The point of all this is that even at 90A it'll probably take a while to trip your breakers, unless the unbalance effect is really large. Unfortunately, there's really no getting around the gradual curve imposed by I^2*T. If you can, I'd suggest choosing a fuse based on what your batteries can handle. If they can handle a max of 200A for 15s, you probably want to find a fuse that'll blow in 10s or less at 200A. That provides a maximum rating, your continuous draw is a minimum, so pick something in between and you should be safe.