I can appreciate them trying to limit scope, but really we should be looking to serve both Ipswich/Norwich AND Stansted (even if that means a separate project will be required to fully utilise things aka. a second tunnel and perhaps extenstion to Braintree), and that means one service is going to need to reverse somewhere. The southern bays at Cambridge are (or at least, used to be when I last went that way!) pretty heavily used already, so capacity may be an issue there, whilst the northern bays are lightly used, though have been shortsightedly shortened for the new footbridge. If you had to reverse at Cambridge, then I'd argue sorting out the northern bays made more sense. That said, coming from the south you can now reverse at Cambridge North, so perhaps that's an option, be it from freeing up the bays at Cambridge itself, or heading north to using them there.
I don't buy the northern busway argument - there are plenty of alternative road options to maintain connectivity (which may, arguably, actually improve connectivity), which you choose is obviously dependant on where the rail alignment reaches the route. My money would be to divert the busway down through Orchard Park from Histon. It can run along Kings Hedges Road to Milton Road and then continue on its current routing, leaving the current alignment free for EWR to reach Cambridge North. It's going to increase costs, but getting four tracks down from there to Cambridge would be worthwhile in the long-term. That said, until Cambridge North opened this section of track was much quieter than the section south of Cambridge, so surely paths could be found for EWR to reach Cambridge station on the existing tracks?