Hi Matt - Diesels hate short runs but this should not be a problem as long as the regenerations are permitted to complete. Is yours an auto or manual gearbox? The reason i ask is that mine is auto and very seldom gets run past 2k revs short shifting for economy. When mine is doing a regen the only real indication I see is the engine ticking over, when the car is at rest, at 1k revs instead of 800. When I do notice this what I do is put the drive mode into sport so the revs are kept higher before shifting - increased engine revs = more heat and gas flow to assist with the regeneration process. If yours is a manual then just hold onto each gerar a little longer before shifting up.
I used to worry about shutting the car down when parking up at a destination but the car seems to be able to cope with this and commences regens on the next journey. Yours may regen more often due to the shorter journeys.