It does seem a little excessive, but think KI is encouraging us to utilize other members of our crew. The way companions are managed now, many of your crew may never see the battle board because they are not in the 'top three'. If one of your favorites is knocked out, pull up another companion for a little while. KI has supplied us with lots of powerful companions and doesn't want them to go unnoticed. Who knows, maybe you'll find a new favorite?
Also, try training a few of your favorites in ranks of 'Scrapper' this will reduce the amount of time for recovery. Did you know you can send your wounded companions on task? This way, they can still be useful for you.
Cool down depends on the level of the companion. (I think. It might be of the pirate on whose crew said companion serves) At the point you're having to cough up that much gold, you're a pretty experienced pirate and should be able to get that amount easily enough through farming or by sending out your other crew members (you should have a lot by then, too) to plunder. The lowest level pirates only need to wait a minute or two for their crew to recover, but they also have rather fewer crew to work with.
I don't find it particularly excessive to pay a lot of money or require a lot of bedrest for a high-level companion. S/he probably soaked up a ton of damage -- if you'd taken the equivalent real-life damage, who knows how long you'd be in hospital.
The idea is for us not to use our crews up like tissues, but to be the sort of captain that uses strategy over brute force to win a battle. If there is a major cost to sheer bloody-minded whaling away at the enemy, that means that at least some of us are going to be playing smarter to avoid paying that cost.
I'll admit, at first I was a bit sorry to see the life-fountain restoring all the crew to full health go away, but I actually prefer this way now. It adds a dimension to the game that was lacking when I knew I could just go tap the nearest life fountain and get everyone back.