After almost a year, the RCA and the Israeli Chief Rabbinate have a deal worked out.
Link to the press release
Looks like everyone got their cake and gets to eat it, too. Rabbanut gets the RCA to get serious and tough on conversions. I've done a conversion with R' Freundel, and know that he's serious about giyur standards. RCA gets to remain the address for orthodox conversions in the US. Everybody's happy.