i did a bit of research on this for you and although the data is limited there seems to be no great harm recorded to babies where the mum has taken metformin throughout pregnancy. There was one suggestion that it can slightly increase the chance of pre-eclampsia but this can be carefully watched for.
It seems that babies born to mums taking this medicine are of normal birth weight and grow normally. The only problem occasionally is an increased risk of jaundice which is successfully resolved with treatment if necessary. If your specialist has experience with metformin and PCOS and knows what to watch for I think you can be confident in their recommendations.
This is the page for this stuff from the medical journal of australia. Its a bit clinical but basically says the above
Leanne, NZ, Ella age 2 & Sam age 6months