From Scunthorpe, it's just as easy (and roughly the same price) to get to Manchester Airport as it is to get to Humberside airport if using public transport. I see no reason for the Cleethorpes - Manchester Airport service to bu cut. Perhaps shortened to Manchester Piccadilly, but other than that, I see no need for any changes.
It has been mooted that Manchester Airport-Cleethorpes could be split into two at either Sheffield or Doncaster as part of franchise re-shuffling, but I cannot recall the source for this at the moment.
The source is somewhere on the ORR or DfT websites, but I'm not going to go looking for them, but to me, terminating at Doncaster or Sheffield doesn't make sense. While there isn't many people who do the whole journey from Grimsby/Cleethorpes - Manchester, there are some. The main flows* along the route are Cleethorpes/Grimsby - Doncaster/Sheffield, Scunthorpe - Doncaster/Sheffield/Manchester and Doncaster - Sheffield/Manchester.
The ideal situation in my opinion would be for the TPE service to terminate at Scunthorpe instead, with Scunthorpe - Cleethorpes and the Barton branch handed over to EMT. The reason I keep suggesting this is not because it is local to me, but instead down to the fact that the TPE service is usually reasonably well loaded from Scunthorpe (especially the 1008 service which is the first valid off peak service to a lot of places), where as the number of passengers from Grimsby, Cleethorpes and Barnetby to Scunthorpe will usually fit into a 153. The alternative is to have the TPE service terminate at Scunthorpe, with hourly Sheffield - Scunthorpe stopper extended to Cleethorpes
Also, there is plenty of room at Scunthorpe for the approaches (from both sides) to be modified, and a new platform (if needed) to be constructed to handle terminating trains.
In my opinion, it's a win-win situation all round. Yes some passengers will lose out, but the main bulk of the passengers are catered for with a (semi) fast service, and TPE get a slightly smaller network, something they are always after.**
* I'm not going on any official figures here, just on my experiences on using the TPE service from Scunthorpe. Some days, the train empties at Doncaster, with more people joining there, other days, most people stay on and carry on to Sheffield and Manchester.
** I saw a post made on wnxx a couple of years ago which was made during some strike action. TPE were only running Manchester - Sheffield/Leeds/Preston to which someone replied that's their dream franchise!