CR is really only a hassle when you're new to the game and dont know how to manage it yet.
1) There are certain skill specializations the player can take to minimize its impact. If you want to engage in a lot of heavy combat, you need to select skills that make that an efficient behavior for you. There are a number of different ways to go about this, but the most straightforward is to simply spec into the combat tree to make the player ship strong, so you need to deploy fewer ships, and take fewer losses. In addition you could specialize in powerful carrier fleets, or industrial fleets that allow you to deploy and repair ships for reduced cost.
a.) There are also skills that drastically reduce the cost/length of repair, supply use, and fuel consumption, making upkeep a simpler matter to manage.
2) With greater player skill it ceases to be much of an issue, because you'll be better at winning combat more quickly, with less hull damage, and with fewer ships, enabling you to distribute CR costs among a smaller variety of ships.
3) Fielding fleets that are specialized for a specific purpose, rather than trying to do everything in the game at once with the same fleet is also an excellent way to keep costs down. Unless you are just fighting willy nilly in a war zone, on a typical mission run the most frequent you can expect combat encounters to be is one or two at a time, and it's really not difficult to field a fleet that is efficient for that purpose, and will be completely "healed" by the time the next combat occurs, without having to pay the upkeep on a bunch of ships that are not contributing to your combat effectiveness.
Otherwise, you must accept the reality that the game does not want you to be able to fight indefinitely, and running away from some battles you are not prepared for will be a necessity. I did plenty of running away in M&B.
