i dont suggest that you use a cruiser as a science captain, just stick with a science ship or you will be blown to bits by a BoP. the cruiser will only give you more hull points and 2 more guns, but all those scoence abilities you will be losing will nerf your ability to do damage.
ENGs and SCIs can be put to work on almost every Ship if done right. So SCI and Cruiser can work. The only class that "has" to stick to the ship category is the poor tactical, and even here the others can preform better at times.
I have a science captain and I fly whatever I feel like (no real favorite available at tier 5), and cruisers still are not squishy even though I'm not an engineer, nor are my escorts (at least any more then you'd expect. You can fly what you want, just either spec yourself generally, and realize you won't have that extra hull and shield strength, or spec yourself into your ship of choice and fly whatever.