If it's possible that it's stuff that's being used at initialization time, wasm-ctor-eval might help.
Also, you probably want to build a reactor (-mexec-model=reactor) if that's not what you're already doing. A command will use WASI to read command-line arguments and environment.
But it's hard to tell without knowing the specific imports you're trying to get rid of.
This is what I've been doing for my little non-WASI runtime. For my minimal programs I find only a few wasi exports are required, which don't appear to actually be used and I just stub them out. Would love to figure out how to get rid of the code depending on them entirely but it's lower priority.