Now, I've dealt with that before
First thing, how devoute is your character. Just cause you serve the church, doesn't mean that you arn't without your own moral compass. If you are a zelot, then you should kill the trolls no matter what age they are. They arn't animals, they are born evil "if you had been tied down, and the trolls offered you to their children as food..would they eat you?" If however youg doing all forms of magical creature as "animals" unique or otherwise, then you can make an argument that they are only doing what is in their nature, and that they are inthemselves not evil. I tend to say however that all humantype creatures are a byproduct of D&D evolution, they are then a race, and have in them a nature which, for trolls is evil unless otherwise stated. Just like half orcs, or orcs sometimes due to DM tellings, a troll may or may not be evil. you said however that these babies felt Evil to you, if confirmed with your Dm that you magical ability, through the divine is telling you that they are evil, then you must make a choice. Do you agree, or not. If you do, then their is no wrong in slaying them, if however you feel that there is a prob with this logic, then you shouldn't and now you will find your character in a new realm where he is no longer a solider of his god, but a Ronin....and that perhaps will open much better roleplaying.
I would say that it is easy to go along with the fact that you could kill the creatues and justify it, but perhaps its not where you wish to take this charcter. Or you could kill them, or only one, and afterwards have issues with it that you can use in your Roleplaying.
Use this option that the Dm has left open for you,and hope that he knows the extent inwhich you can take it for the fulfillment of your own adventure and growth as a player.
Game on.