If it's warm enough for you to be cleaning the pond, when you clean the sludge from the bottom, just put it in a garden bed - if there's anybody living in the muck, they'll figure it out. These wild critters aren't as dependent on us as we like to think they are - I mean, they found there way to you on their own, they'll figure out what to do next. That's always been my approach anyway. I kind of keep my needs on at least an equal footing with the frogs - if I have the time to get a job done, I'm going to do my best to impact them as little as possible, but I'm still going to do what I need to do. And quite honestly , every spring we find a couple of frogs that stayed in the pond and didn't survive the winter, so there's no guarantees that they will make it even if you leave them be. Nature has a way of balancing this stuff out. Ultimately they would most likely prefer you leave the whole pond as is, but you get a say too!
We'd love to see pictures of your pond! Show us before and after so we can OOOOOHHH and AHHHHH at your hard work!