Of COURSE we'll screw up royally:
There is no way that there won't be massive harm done to these children - at least for the first couple generations. But biology is cruel, ruthless, and selective. After a time, we'll figure out how to deal with them. The process will be ugly, however.
Human beings have a long history of learning to deal with non-human children - they're called domesticated animals, or pets. If the process is anything like that, then there will be gruesome mistakes as we poison children, drive them psychotic, create imperfect incubation conditions so they have horrifying developmental problems - and all that is assuming your aliens are derived from a panspermia event, so terrestrial biology is essentially IDENTICAL.
Science, done the way it's been done for most of human history, will have a large number of aliens raised like chicks in an incubator. The conditions and inputs - nutritionally, socially, educationally, etc. - will be varied and evaluated. Very large numbers of these aliens will die simply because we don't realize they need large amounts of something basic, like huge doses of lysine. Then there will be screw-ups where they die from terrestrial infections that creep past isolation lines, OR they need symbiotic bacteria we fail to provide.
And of course, even if we're wildly successful, the best we can hope for is a bunch of alien children who have been humanized to the point of being unrecognizable, and possibly traumatized by the bizarre upbringing in a giant petri dish.
But after a few generations, we will find an accommodation with these beings, dealing with their quirks, exploiting their strengths and weaknesses. If we are extremely sensitive, we may eventually separate them from us and allow them to set up a society to their liking, so they can deal with us on their own terms.
More likely, we'll treat them like second or third class citizens because they are unable to conform to our standards. But hopefully we won't make them slaves or pets.
"Hey, Spot, come here! Good boy! Here's a lysine treat!"