There is stuff that will eat rust.
I'm doing some experiments with Evapo-Rust.
It is supposed to be non toxic. And can be reused for quite some time (although it does chelate the rust, and presumably will eventually get less potent).
If you can wire brush off the heavy stuff, that will make it quicker acting, and potentially make it last longer.
It does leave a bit of a residue, so I'm not sure I'd use it on a completely closed system. Check what materials you have that it will be in contact with.
There are also acid based rust cutters. Many are Phosphoric Acid based that are supposed to create an impassive coating. However, I'm also concerned with loss of material.