If you have decided your rockers have enough structural integrity to either "be safe" or to "live with"
1) Rinse the cavity out with "MetalReady" (a Por15 product which converts iron oxide to a phosphated zinc) Be sure to have a catch basin under the weep holes/rockers to catch all of the MetalReady, as it can be saved and re-used.
2) Next rinse with de-ionized water (catch that junk as above and discard at your local recycling station)
3) Next rig a high-flow hair blow-dryer (1500-1800 watts should do it)
so that it blows in there to thoroughly dry it all out, give it a few hours.
3a) If you are putting patches in, you may chose to do this now, but you will need access holes (small) to reach into the cavity for the following steps. These holes can be cut in an obscure location and after you are done plugged with a genuine BMW Gmbh plug!
4) Get a source for the yellow zinc phosphate paint, and paint the entire inner cavity with the stuff. If you are insecure, give it a couple of coats after letting the first tack up for a few hours. You will need a wand-type sprayer to reach in there. Be sure to have ventilation better than you ever thought you would need ... this stuff is nasty to inhale. Good idea to use a full-face chemical respirator to be on the safest side.
5) You may find the wand helpful in application of the MetalReady, also when you go to rinse with the DI water.
6) Do NOT be tempted to use the blow dryer after applying the zinc phosphate paint the yellow zinc phosphate paint. You just have to be patient when awaiting setup and drying. Ideally you resume work when you can no longer detect fumes (remember its nasty, so give it some real time)
7) In case you are wondering why you can only use the yellow zinc phosphate paint, its the only stuff that works. It will complement the MetalReady by penetrating any voids that might have been missed, you REALLY want to get all the iron oxide (rust) converted to inert and the yellow stuff does that. Don't be tempted to skip the MetalReady rinse/prep though, nothing quite like bubbles appearing under your shiny paint 2-3 years after you finished the job.
Hope this helps