It is harder to control the cooking in a microwave.  There are a few things you can do.  Add more liquid, use a lower setting on your microwave and stop to check the progress more frequently.
Personally find that they taste much better made on the stove top.  Creamier, can get the consistency just right.
And honey is a natural sugar, but its still sugar.  If you were a diabetic you would have to treat it like any other simple sugar source.
There is a 'fake' honey that you can get, just can't remember the name of it.  Expensive, but has the flavour and texture without all the sugar.  Other option is to look for sugar free maple flavoured syrup.  Again, not the easiest to find, but specialty retailers tend to have that sort of stuff.