@Sciencius Your point pricing aside (which I agree with) I think your example is really showing the importance of player choice in game design. You want to make sure the player is presented with reasonable decision points during the game and that the opposing side has the ability to respond reasonably or be able to prevent the situation with their own previous decisions. Your upgrade card certainly takes away all the agency of the defending player (which is bad) but in addition it effectively takes away the decision of the attacking player as well (it's going to be very likely you target the most powerful ship every single time).
So yes -- no amount of point balancing can really save poor game design. Unless of course you simply price it out of the game completely as a whoops-an-upgrade.