This is why I think most or all EWR trains should run via MKC with a reverse, and why a north to east chord is necessary.
I do agree that an eastern link to MKC would make a lot of sense and probably should've been done from the start. Although MKC won't be
that much of a major hub, as HS2 will divert most of the long-distance trains away and most commuting traffic to the city is, and most likely will always be, by car, this argument would make sense if they were proposing e.g. 4tph to MKC, which may be overkill, but at the moment there aren't even plans for 1tph from the east. It's more than busy enough to have at least
some link that doesn't require a change at Bletchley (or double-change to get to Cov, Northampton or Rugby).
Though I don't understand your logic behind diverting all services that way. There really isn't (and won't be by 2040) the demand for 4 trainloads an hour of people from Cambridge to Oxford or Bicester - 2tph is more than enough for an interregional service assuming the trains are at least 5 cars long. A triangular network centred on the future Bletchley triangle, involving 2tph on each of Oxford-MKC, MKC-Cambridge and Oxford-Cambridge (plus 1tph MKC - High Wycombe) would make a lot of sense and get a lot more out of the multibillion pound infrastructure than any Stewartby terminating shenanigans. A direct service to central MK would also make the Marston Vale station rebuilds feel a lot less like a waste of money.
It is a shame in this context that Fenny is closing, though. Perhaps consideration should be given to reopening it if this plan goes ahead, so Bletchley isn't left with a railway line that runs through it and may be useful to some but which has no station. Obviously there's no way to serve Bletchley station without the reverse, but you could at least serve a station in Bletchley to allow for established flows, unless you only sent some trains to MKC and thus would have the option to send one an hour to Aylesbury (though realistically Aylesbury-MKC would be of more use).
There are hundreds of rail lines in the country that pass through a fairly busy urban area with no stops. I agree in principal that we shouldn't be closing stations with no replacement post-2000, but if you do want to get full potential out of the (much higher potential) longer-distance city links that EWR will create, then you're left with no space on the MVL for stopping trains.
I really don't think keeping the MVL stopper at the expense of 1-2 long-distance paths is a good tradeoff, and the cost of making the line e.g. 3 or 4-tracked to maintain a local stopper would be a few hundred million pounds for only a few thousand annual passengers. Of course as a supporter of rail growth I'd have been all for that, maybe you could even run the stopper as a tram-train into MK city centre to get the most out of it; it'd be a way of sneaking mass transit into a city that won't pay for it, Cardiff-style. But I don't think the wider UK populace would've taken too kindly to an extra £1 billion being added to the EWR project just for the MVL locals.
The stations planned to be closed currently have around 100,000 combined annual users - even if we assume 50% growth in the next few decades, that's still around £7000 spent per Marston Vale line passenger. Not a good look, when you could just close the stations, rebuild the existing ones with a big car park, and move on.
Even if you do accept that the MVL stopper's fate is likely sealed, not exactly sure why you'd need a station on the Bletchley north-east chord. The town (or is it just a suburb now?) will still have a minimum of 2 trains an hour from Oxford to Cambridge even if the chord is built, which is plenty for the Bletchley - Marston Vale/Bedford/Cambridge flow.
You're more or less asking for semi-fast long distance services to serve a secondary station in southern MK, which would be very different to e.g. Cambridge South (which is an actual destination). That's what urban mass transit should do the job of, in the same way that semifast long-distance trains from London don't usually serve zone 2 interchanges, because the tube ride from a central London station is really straightforward. MKC should be a major urban transit hub in the city instead, with people in the city connecting from bus/bike/car to train there, which would make a lot more sense than getting EWR to provide the main urban transport connection from Bletchley into Milton Keynes. The layout of the city doesn't really lend itself to a good bus network unfortunately (although it'd be great for a dense light rail network, impossible as it is) which is why things are as they are.