Honestly, this is a situation that comes up way too often "late game"....
I will preface this by saying that even tho I play with faction mods, I don't use any balance altering mods and always only use purely vanilla ships and vanilla weapons in my own fleet. And honestly, I have the opposite problem. I feel like my ship is a bit too strong after I take all the combat related perks. You need to think about different approaches to combat and loadouts.
But it didn't matter, since after nearly fifteen minutes straight, all my ships had CR'd out and retreated
The way to take on multiple deathfleets is to do it over multiple engagements. Just retreat, and redeploy again. You only lose 20% CR maximum on high tech ships, less on midline/low tech ships. That means you can deploy them 3 times before even getting to malfunction territory. Have multiple copies of your flagship in your fleet, and you can redeploy however many times you want. That's what I personally do, and I find this strategy to be a bit overpowered honestly, and I'm thinking about making a forum post about it.
My personal flagship of choice is either an oddysey or a Doom, and I always have 2 exact copies of my flagship in my fleet for this purpose specifically. I can do 6 deployments before malfunctions, and I have a spare if I mess up somehow. And I always take the skills that raise my CR to 100%. Against fleets like these I deploy my flagship solo, or with a very small carrier escort that stays way back, and I kill like 20-30 ships per deployment, and retreat before the CR decay starts.
Behold.
https://imgur.com/GTe1Of4That's 5 remnant fleets in a level 3 beacon system, and 3 of the the fleets are the big ones. I purposefully pooled all those fleets together to fight them at the same time.