For your question I'll ask another question to be the answer to your own question. If an atheist learned Latin, would he be on the good side with God? (I suppose God doesn't have a good and bad side, for He is all loving) Now if your intentions to learn Latin is to read the Bible in a better context, and your doing it to be closer to Him, then you would be on the "good side" with God. But if it is just to learn a language, it doesn't matter.
Here is some reference in scripture. Genesis 11:1-8 might help. God WANTED to spread tongues (languages). So God wouldn't need you to learn Latin.
1 Now the whole world had one language and a common speech. 2 As men moved eastward, they found a plain in Shinar and settled there.
3 They said to each other, "Come, let's make bricks and bake them thoroughly." They used brick instead of stone, and tar for mortar. 4 Then they said, "Come, let us build ourselves a city, with a tower that reaches to the heavens, so that we may make a name for ourselves and not be scattered over the face of the whole earth."
5 But the LORD came down to see the city and the tower that the men were building. 6 The LORD said, "If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them. 7 Come, let us go down and confuse their language so they will not understand each other."
8 So the LORD scattered them from there over all the earth, and they stopped building the city.
I guess I should also suggest trying to take Hebrew or Greek. Hebrew was the original language of the Old Testament. Throughout the years things have been mistranslated. Same with the New Testament in Greek.