My subframe was rusty too and looked quite bad when the sill work was done but the guy said it was actually okay if you knocked off all the rusty top and rust-eater it. When he finished it seemed to come up okay to be honest and it was solid under the rust. Yours could be the same and just need a really good go at with a hammer, wire brush and rust eater.
For me it was the sills that were the expensive bit but then the rest of the car seemed to be solid. Seems on these cars the sills by far take the brunt of rust issues. Personally I think your sills need doing even if the MoT guy passed it. As the other guy said, if you want to keep it long term you need to tackle this sooner rather than later.