Bit of a stream hijack here but I've been through the exact thing with my daughter.
She'd been having small amounts of milk on cereal and in baking etc a couple of months so we didn't think adding it to her bottle would be an issue but once she started getting it in larger quantities and more regularly she got an upset tummy and constipated followed by an anal fissure followed by being diagnosed anal retentive followed by months of laxatives and us having to hold her and massage everytime she had a bowel motion so she would relax and let it out (otherwise she'd become constipated again) - poor wee girl!
We took her off cows milk for awhile and gave her goats milk instead (which is mostly made of A2 beta casein proteins). We then really slowly introduced cows milk again (about 20mls per bottle initially) until she was only drinking cows milk. This cleared up the tummy issues but unfortunately the damage had already been done in her head and it took us heaps longer before she stopped being anal retentive.
Another alternative to goats milk is to try A2 cows milk which is similar in makeup to goats milk as it has less A1. We used this for my nephew when he was diagnosed lactose intolerant and it was fine.
Both kids grew out of their milk issues really quickly but definitely reduce his milk intake until you can be sure it's ok (sticking haemorrhoid gel up the anus and feeding your baby laxatives so they constantly have diahorea for months on end is not fun, believe me!).
OK stream jump over