Guinea's picking on baby goats

Picking on them as in causing them to have open wounds?  If that is the case then your only option is to separate them.  Actually, even if there are no wounds, if they are just constantly running after them and pecking at them I'd still separate them.  Nobody wants to be constantly harrassed.

How many Guineas do you have? And how old are the baby goats? Kinda sounds like you may not have enough Guineas to keep them focused on themselves as a flock and the males are focusing their breeding season hormones and aggression on the baby goats instead. Could also be that because the baby goats are new to your farm the Guineas see them as intruders or a threat at this point. 

I'd chase the Guineas off and coop/pen them up when you see them picking on the baby goats. Or just coop/pen the Guineas and leave them cooped/penned for a few days to see if you can break the habit. If you are talking about really young baby goats, then that will give them a little time to grow, develop their agility/coordination and fast reflexes. Eventually the baby goats will grow to expect the Guineas' aggression, and it may become a game to them (and a reason to get all silly running and bucking like baby goats do, lol). 

I've never had this issue, all my Nannies have never let anything anywhere close to their kids and were always protective of them... not even their offspring from the previous year!

Mine do all eventually end up co-mingling just fine tho, and the Mommas relax... hope yours do too!

My goats often wonder into the guinea pen in search of food. The guineas yell & scream @ them. The goats never notice, and if the goats get tired of the guineas they will head but them. The goats will be fine, I would worry more about a goat stomping on a guinea than a guinea hurting a goat.