I don't see the problem. His contract had expired, they offered him improved terms a few times and Jokanovic held out. They decided they'd reached their limit and looked elsewhere.
As for the Brentford story, alluded to in the OP, again it's not reflective of what happened. It's hardly surprising, given the ongoing media "narrative" that's been peddled. Warburton has done a great job at Brentford but the owner, Benham has clear plans for the direction of travel for the club as a whole. This included the installation of a continental style DOF (not to be confused with an Irish style BOF) at this point in proceedings.
Warburton had a one-year rolling contract, at his behest and when Benham said he was pulling the trigger on the DOF appointment, he gave Warburton the opportunity to stay under the new structure. Warburton declined, they both shook hands and Benham went to work on finding a new Head Coach (appears to be Marinus Dijkhuizen from the looks of it). It drives me cracker to keep hearing that Warburton was sacked. He took the job in the first place, knowing the direction of travel and when it got to a certain point, he jumped. Simple-as.