Sure, using repair time as your major cost factor works. Especially on large ships in a mature game.
If time is going to be your major cost factor, you can slow down MRT by increasing the Time Step (id 412). The Time Step is the number of seconds that the Artificial Life script pauses between repair checks. If you double the Time Step, then you double the amount of time between repairs.
(Don't make the Time Step much lower than the default of 15 for performance reasons.)
(Increasing the Total Effectiveness Divisor (ID 411) will do something similar.)
MRT will automagically consume both resources and credits if you supply some resources (but not enough to complete the repair job). So, if you supplied enough resources to do half of the repairs on your Osaka, then the marines will consume the resources first, then charge your account for the rest of the costs. It's not exactly the same as charging BOTH resources and credits on each Time Step, but it doesn't take any development work, either.
If you are getting resources for cheap, then you could increase the overall costs of doing repairs (ID 4). The default of 4 means that MRT charges very approximately
40% of the cost of shipyard repairs. Changing that to 10 would make MRT charge the same as shipyard. Changing to 20 would double the cost of MRT repairs vs shipyard, which might make sense to some players.
IDs 3001 and 3002 work similarly for spacewalk repairs. In this case, the numbers work as a ratio. The default values of 33 and 100 mean that spacewalk repairs cost 33/100 (33%) of the cost of shipyard repairs.
As you can see, there is quite a bit of flexibility built into the t file, without requiring any code changes.
I know that some players like salaries. If millions of credits in training and repair costs are not enough for you, then, sure, knock yourself out. But the easy path is to adjust the repair costs to suit your game.
One other thought for you: An alternative to docking at a station would be docking at a "Repair Aran". You probably know that you can get an Aran by hunting in Undefined Space (with an Unfocused Jump Drive, UFJD). Arans are the only ship in the game that have a mammoth capital ship docking port, so you can dock any other ship to it. (You may want to be in another ship when you dock them to avoid collision damage.)
You could then keep a crew of marines and a stock of resources in the Aran for doing repairs.
Arans don't move very fast, so I think of mine as a "station that can jump". That might be handy for post-battle cleanups. You could repair captured ships without needing to give them jump drives. (Of course, you will have to defend your Aran because it has no weapons and is a giant target.)