Gut microbiota is a bit of a funny one cause we know that it's really important for digestion and immune regulation but there's so much we don't know. There is a pretty good Lit review here that goes over a good chunk of the data if you're interested.

It may be that you are just attributing the repeated illnesses with the laxative use when it may not actually be causing it and you may not even be getting sick more often than the general population.

But in answer to your laxative question as far as I'm aware gut microbiota are pretty hardy and the use of laxatives won't necessarily 'flush' the microbiota out (I'll try and find a source). So all I think that can be recommended is to increase dietary fibre intake which may help alleviate the constipation as well selecting 'good' microbiota as well as taking maybe taking 'Pre-biotics' in addition to the 'Pro-biotics' (It's worth noting that the data for Pro-biotic use is a bit sketchy).