I was going to mention vanilla--I see Heather beat me to it. My kids sometimes still ask for "vanillamilk." We don't drink milk, except a vanilla milk treat occasionally; I use the lactose-free organic stuff in my cooking (I was SEVERELY lactose intolerant for a long time and breastfed for a long time ... I never had milk around ... although cheese and ice cream, for my then-husband were also available to the kids :) ).
The "throw away food that has been left out for two hours" is the CDC(?) recommendation based on people getting sick from picnic foods (which (1) usually are in warm environments and (2) usually have large germ exposure). I'd say milk in a sippycup, particularly if she is carrying it (so, 90+ degrees), meets both high-growth-rate germ criteria ;).
That said, I used to be freaky about throwing everything away that had been left on my counter more than a couple of hours (a lot of the year my house is 65 degrees, and most of the items in question had been boiled and then only been touched by a serving utensil ... really, very low risk) ... and then my then-husband visited His Cousin the Famous Doctor and testified upon arriving home that their family (also of many kids) would leave dinner or even lunch from the day before on the counter and then eat it the next morning. This rocked my hyper-worried world ... but I am more relaxed and realistic now ;).
Obviously, I Am Not A Doctor and this should not be construed as medical advice ;) ... and frankly we do occasionally get bouts of food poisoning (although I don't think any much more than we got back under my old rules ;) ) ... but logically, if you've killed all the bacteria (all storebought milk 'should' be sterile or nearly so) and haven't introduced significant new bacteria (don't open the container and then later shake the milk, for instance, and don't drink from the carton ;) ), it should take quite a while for newly poured milk to gather and then grow a significant population of bacteria.
Back into the fridge: food safety experts probably scream no, but again, logic applies. Putting it in the fridge slows but does not half whatever bacteria growth is going on. So, if she's had it for five minutes, you're good. If she's had it in her warm hands for an hour and 45, you probably aren't going to get effective storage (bacteria inhibition).