This bug makes very little sense to me. The Steam version of C2 is for all intents and purposes identical to the standalone version. The sole difference is that it doesn't read a license from c2license.txt like the standalone version, it communicates with Steam. It seems unlikely this relatively trivial change could cause such a serious degradation of performance over time. Further, the autosave system is certainly identical between the Steam and standalone versions of C2, so I am at a loss as to what the problem could be. I presume it must be something about the Steam client or the way it launches C2. Further still, as far as I know most Steam users use it successfully without this type of issue, so it seems unlikely that we could reproduce it (and I never have).
I think Steam does some things to the programs it launches. It's designed for games and the "in-game Steam overlay" is enabled by default. Turning that off is almost certainly a good idea since it's designed for games and might just be incompatible with C2. I think it does some other things though, like at least timing how long it's running for play time stats, and possibly other behind-the-scenes alterations. I have no idea what any of these things could be, what to do about them, or how they could interact with autosave to cause any problems. (Autosave is basically a lightly modified version of the 'Save' button that just directs the result to a different file. If the problem does not reproduce by clicking 'Save', then I am pretty sure it really is just a random problem that only interacts with autosave by chance, rather than actually being anything specific to autosave).
The symptoms sound something like a memory leak, but from the numbers you have reported, there is no corresponding increase in CPU or memory. I'd expect either the CPU usage would keep increasing (such as having to process a longer and longer list every frame), or memory usage keeps increasing (exhausting memory, caches and falling back to disk). Either would explain degrading performance, but neither seems to be the case. So no leads there either.
I'd email Valve but they rarely email me back. These days they have thousands and thousands of developers using the store, and their focus is probably on their AAA games.
If you are happy to work around it by disabling autosave, then that is OK I guess, but I feel like it's probably a random issue that may still happen in other ways. If you absolutely cannot use the product at all, then unfortunately we can't issue a refund, since all Steam purchases are processed by Valve - your only course of action would be to obtain a refund for Construct 2 from Steam and purchase again directly from our site.