Well I can only offer the obvious response because I've been forced a number of times to do this myself, re-record it the way you want it to sound. The easiest way to solve the problem. I'm a natural hard hitter, unfortunately, that goes for every instrument I play, and I constantly have to remind myself not to play with power and force.
So the obvious answer is what you already know, if you do want a softer sound with the steel string, more like the nylon (or just record the nylon?) , you will have to re-record it, whilst playing softer. There's no way around it. Sure, you can modify it and make it softer to the ears, with EQ, comp and even a transient designer, but you won't fully be able to take away the chugging, because you or your friend, whoever it is playing, probably is doing just that, chugging.
But I'm in the same boat, I can spend days trying to make an instrument into something it isn't only to realise way too late I should just re-record it the way I want it and be done with it. Usually only takes 15 minutes to get it properly recorded. Then of course I go through the very same process on the next song...
With that said though, it doesn't sound bad in my ears, a little attitude is always a good thing! Hehe, just to make it easier for ya!!!
Cheers,
S