Frankly we were always designing the
Darwin with more teeth than I think was necessarily strictly called for by the brief for a science vessel in the expectation that it would be fighting. It is flatly better than the Newton anyway, so people should be happy IMO.
But honestly the issue is less here what is happening in game, and more that this has been built up as a major event, treated as a major event, and then we have a total removal of player agency. This is not how the Earth-Romulan War, where we felt very much involved and that our decisions could effect the outcome. Of course players could in theory know that there previous decisions would alter things, but given the goldfish attention spans of questers, this was never really realistic, and even then, we're still talking about a timespan of four years where we're just sitting with our hands tied.
If this is how you're committed to treating it then I'd actually agree with
@Wootius and ask that we try and skim/timeskip over it. Three more updates of watching Starfleet get chewed up whilst we're impotent is not fun, and even the players loudly claiming they're okay with it because they want to argue with me are not actually going to enjoy it in reality when it happens.