From Stevenage, Thameslink run a 15-minute semi-fast frequency taking up to 30 minutes (as well as Great Northern's half-hourly stopper taking 40 minutes), as against LNER's half-hourly service taking 24 minutes.
Passengers travelling from Stevenage to London have a decent alternative in Thameslink, and while yes it will add a bit of time to some passengers' journeys, it won't be a huge inconvenience. Passengers travelling from Milton Keynes to London don't have a decent alternative on West Midlands, the service is irregular and for the most part much slower, so yes I would support any MKC passengers in their uproar if Avanti withdrew the option to use their trains for that journey!
There is a frequent Thameslink service from Stevenage but there's often disruption. Take last week's issues following the power failure at Blackfriars, LNER services were very useful but I'd imagine they won't want to assist once services become pick-up/set down only.
Making Stevenage passgers take Thameslink will just mean that those trains are busier. They are high capacity trains and they will cope - for now but I suspect things will be tight, especially mid-week evening peak.
LNER between Kings Cross and Stevenage typically takes 21 minutes, Thameslink from St Pancras takes either 27 or 30 minutes (depending on whether it's a Cambridge or Peterborough service). Perhaps a first world problem, but it is an increase in journey time.
LNER has clearly wanted to serve Stevenage in the past, even to the point of having cheaper dedicated fares. I've long regarded these fares as ridiculous but they will lose their share of the fares income between Stevenage and London.
St Pancras low level platforms aren't always the best place to wait for a train, especially when there's disruption. There's no phone signal (to be fair there is wifi but it's about time a phone signal was provided). Once of the escalators from the southbound platform has been out of order for weeks, I don't know why the remaining escalator cannot be reversed to take passengers up from the platform?
Although from December there's trains to Kings Cross 0702, 0749, 0801, 0902, 0919 then your 5-9 minute gap every hour from 0956.
Good luck trying to stop passengers boarding at Stevenage. Thameslink and LNER trains will be either side of an island platform. Local door operation isn't an option due to the numbers alighting from the north (very healthy numbers these days). Will the station staff start shouting at passengers or will it just end up being allowed for 'those in the know'. I can see the 07:02, 07:49 and 08:01 being particular issues, especially when the adjacent Thameslink trains are late or cancelled.