Exactly this kind of procedure happens all over the Northern network, at stations including Hazel Grove, Hexham, New Mills Central, Adwick, Preston, Morpeth, Warrington Central & Bank Quay, Horsforth, Alderley Edge, Metrocentre, Crewe, Chathill, Clitheroe and Ribblehead. Plus at Oxford Road on a Sunday morning, not to mention the vast majority of other operators also do it.
It's nothing new and there's nothing inherently wrong with it. Yes, training and a defined method of operation may be required, but it's really not the end of the world and it certainly wouldn't be a roadblock if that were the way things were heading.
With respect, Stoke is not that busy. You've got 2tph Avanti, 1tph EMR, WMT, XC and Northern. 6 trains per hour each way in total. It really would not be insoluble, particularly given the fact that the through platforms are bidirectionally signalled.
That's probably more the salient point. The 323s are well suited to the line in many respects and there is no real reason to go to the effort of replacing them with something else.