Hello, I have had the same problem with being attacked.
I am playing with the most recent build of the mod, the Dark Avatar version as well as the most recent build of DA itself (not sure which, but I updated just prior). The problem occurred on both the previous version of the mod (the one with seven downloadable files, I think) and the two most recent updates of DA. In my first game, I played as the Federation and in the second and third, I played as Klingons (because the Federation are K'Pla and have no Grum'bah! No, I have no idea what that means.)
The game basically seems to crash irrevocably, without any helpful errors, as soon as I was attacked. It may also be because of the Borg specifically, since they were the ones who attacked me in each case that I recall.
There did not appear to be any slowdowns or anything indicative of a memory problem at the time of crash, and I was able to attack Borg ships at least once without a crash. I wonder if the problem might be when the game wants to go to the "battle screen"? My attack on the Borg fighter did not initiate that and may be why I got away with it.
A few other things that may warrant your attention:
1) The Dominion seem to be using the Borg tech tree and ships, according to their race screen. Every other race has their own unique branches, so I assume this is a mistake on your part. I did not notice, however, if it was reflected in the game as I don't think the Dominion made an appearance. You can see this yourself from the Dominion's profile here: http://www.gc2startrekmod.com/dominion.htm
2) At one point in my first game, with me playing as the Federation, the Klingons took on the appearance of the Arceans in the negotiation screen. They appeared as regular Klingons the first time I encountered them in that game. Is this a bug, or are the Arceans yet another branch of Klingons that Worf is unwilling to talk about?

3) Some of the racial stats for the various races seem out of sync with how I see them in the canon material. While not a problem per se, it might be a good idea to tweak these a bit. For example, the Borg should most definitely have a very high Loyalty rating; as we all know, resistance is futile. They are given a high Morale rating, which is also appropriate to them (or, rather, irrelevant). Cultural influence would be another high rating for them, at least as far as game mechanics are reflected rather than representing other races buying their brand, so to speak; assimilation, and all that.
Anyway, I hope this information is useful to you and I eagerly await the next patch for this already excellent mod. Thanks a lot for putting it together.