Don't worry!The body check undertake in HK is only for sure the Maid is "clean", they've already checked in Indonesian. Now your maid no need to take care of baby, I think 2 days is not so dangerous. For my case, my maid went to my home on Friday and I let her to have the body check on Saturday and the results were given on the coming Monday, during the period she took care of my 10 months old baby and do the housework.
Filipinas are also required to take a compulsory body check. Only when they have a satisfactory report they can leave the country for overseas jobs.
However, we usually ask them to take another body check again as we don't know the standards in the Philippines.
If you insist to wait till the report is out before picking her up, I'm afraid you will have to pay the salary as well as the wait is requested by you. Changing labs in order to have the report sooner may save you 1 day's salary at best.