Forget the money it costs, the fact that the option is available to a player is enough to tip the balance.
I'm sorry but this is just out right wrong. You can't forget the money it costs since that is the whole point. The more expensive unit should perform better under equal circumstance but it ties up more of your resources, making it more painful if the unit is lost. It's a risk vs reward system and a very basic one.
Now please explain how just having a unit in your deck tips the balance in any way? I have units in my deck I never buy and deploy, so how are they affecting anything?
If stars spent instead of level is displayed on MP profiles then I think everyone can be happy. All "levels are is an indicator of how long you have been playing MP. It does not measure skill. If you are playing unearned games and are choosy about your opponents then I think the ladder rank and stars spent are a better indication of what you are going up against. Nothing is broken, and even the basic units when used well can stomp more advanced ones.
If you display stars as some indicator of "strength in play" then you'll just have other problems. What about the guy that spent enough points to unlock the Apache and nothing else? Someone like the OP will look at his 6 star rating and figure he has no units more powerful than a 10 star deck, which could easily be wrong.
Why can't you just assume that every opponent you play might have access to every unit in the game? The units are balanced by their cost and availability numbers, not by their locked/unlocked status.