The Cap Point system in single player can be troublesome but going against the AI I haven't run into any problems, so far, that can't be overcome with clever use of skills. Some factions are definitely easier to beat the turrets with than others.
Possible solution for SP, once all ships are destroyed just end the match with a player victory. This would feel like making things significantly easier though and I don't think it's necessary as long as the ships are still destroyed, your fleet falls back and survives, and you can just attack again the following turn. I will say, though, having alternate game modes would be nice and I'm hoping those will be in the final release. Escort ships wasn't the best but it was a nice break from Cruiser Clash in the first iteration.
In MP it is definitely a balancing factor to add different avenues of play in the instance that you go up against the specific faction/fleet that your fleet happens to be weak against. With 12 factions and different ways to load out your fleets it's very likely you face off against one that you would rather participate in guerrilla style tactics against rather than go head on. If they do add a Cruiser Clash I imagine it would be just like the first iteration, less enjoyable for the lower skilled player due to getting wiped out quickly. Lower skilled players can more easily avoid combat and try to focus on points. Not to mention the possibility of a repeat of one completely overpowered faction that kills anyone's desire to play cause it's not their favorite faction in lore and it's boring to always see [X faction] vs [X faction] over and over.
TL:DR - Don't just knee-jerk remove Cap Points due to a small amount of complaining from a small group and if you do make sure you've taken steps to find better balance of the factions even if it means destroying the lore of Warhammer 40k. Currently removing Cap Points would mean 2-3 factions would be the only reasonable options in ranked.