In order for it to be a threat, the Broncos would have wanted RCW to continue playing without an injury clause. They didn't. They dont. It seems obvious to me, but maybe just plausible to most, that they really just want to move on.
I believe RCW was told they're done with him and, to protect themselves financially, they're benching him. If he wants to take that clause out, then there's no downside to the Organization so that's the only way he could continue to play. In RCWs mind, that's a threat. There's no possible reality where he's not the preferred option over Stidham. In truth, the Broncos wanted to bench him for numerous reasons but were open to allowing him more playtime... but only if the risk was removed.
Whether this is a threat or a favor to RCW is all in the presentation. That will be impossible to prove and would never impose any damage on the Broncos. The entire drama-fest is RCW being himself: the 50mil/yr victim. He hopes it increases his value in Free Agency but, in the meantime, he gets some ego stroke from RG3 and Ryan Clark and other talking heads.
The Broncos are done with him. Their lack of any response tells me they don't see him as even worth the PR group investing 30 minutes to write a statement.