It is an interesting idea, but your explanation points to why your solution may not work.
Here is the jist of your suggestion, I think.
The USA has lots of CVs and BBs because they can afford it. They are using them to soak hits because they have so many, so lets add a modest repair cost to stop that.
Here are my thoughts:
The problem is that the USA is the only power in the game (most of the time) that will shrug off the repair costs. So you may actually make things worse for Japan in particular who would be much more affected by paying those costs.
Also your suggestion that a 1 IPC will deter a player from willingly taking hits from their capital ships right away is a bit confusing. The next cheapest option is to lose a 6 IPC sub. So a 1 IPC cost isn’t really going to change things. But as was pointed out earlier, Naval bases are quite pricey as is and the need to pull back a damaged fleet is still a bit of a deterrent. I think I’m OK with the rules as is.