If you are flying a 1 billion ship, you should not fly it alone. A clever thought out friendly coverage is a must if you want this to work. And it can work out beautifully.
In the first place, such a big and expensive ship should never be able to dominate everything around it alone, as it should be an investment of cooperation with other players, and it all demands team work to succeed. If some guy keeps on grinding to buy the biggest ship alone, and hopes to kill everything, he'll lose.
On the other hand. Gather 4 bombers. Get 2 fighters and a Battleship on the other side. If we assume that these players know how to play, the fighter-battleship group has far more advantages than the bombers. Not only that the bombers will have to keep on firing their SNACs forever to take out that battleship, they'll also be quickly pressured and taken down by the fighters and occasional anti-snub turret fire from the Ship itself.
Clever players can easy deal with 4 bombers WITHOUT a single loss to their sides with such odds. That's winning against 4 players with 3 players of your own, and then keeping it up and taking on more players to kill as you'll all still be surviving.
It's up to you to use your toys properly. The battleship is big and strong as it is, and being big, strong and expensive brings its own disadvantages. It's a rule of nature. You should not break the rules of nature by making such things unchallenged beasts of wherever they are. Use them knowing their innate strengths and weaknesses, then there'll be no problems.
If you focus on these things as you balance, and only put the price tag on the toys as much as the players will keep on buying them, it will be fine. Guess what, everywhere there are battleships still, despite that price. Even CAU8s, when they are simply ridiculous. So the price doesn't seem to be a problem.
Use them knowing their innate strengths and weaknesses, then there'll be no problems.