I agree. Take out the smaller ships first then worry about the big one. If you are grouped with like minded players, popping the small guys takes no time at all. Then as stated before, the big guy is easier to deal with, with everyone focusing their fire on it.....not to mention that if you are in a larger group, you have a better chance of not being fired upon.... or at least for a small period of time.
If you want to rule this red alert, be a torpedo specialist with as many spreads as possible. I run a fleet advanced escort at the moment, with spread III + II, and cannon scatter volley. Firing at one target at a time is a pain when you can be *destroying* multiple at a time. Tholians are swarmers - use AoE ;p