It is unlikely for Rudra to think that Paro had betrayed him because by the way his character has been presented so far, he always has an unexplainable trust when it comes to Paro (I suspect to a certain extend with his mother too).
When in front of everyone , Paro chose Tejawat over Rudra and hit his head, he still wanted to find and protect her.
When all evidence were placed in a way which showed Paro to be guilty of trying to kill his father, he still trusted that she did not do it though outwardly he accused her (Maithlli reminded him of his true thoughts about the fire incident).
I don't think Mohini or for that matter anyone will be able to break the unexplainable trust Rudra has upon Paro,,besides I get the feeling Mohini might already be out of the picture during the separation track. I agree that Paro instead of telling in person may leave a letter for Rudra and after reading again he will mutter stupid girl and start looking for her.
Million dollar question would be where will Paro be when Rudra start to look for her? It would be a interesting twist if they introduce a new character in the separation track. If Paro gets help from V K Singh and wife, Aman or Damayantiji, all these people will definitely inform Rudra and try to get them back quickly that would make the track boring!