Why does Friar Laurence agree to marry Romeo and Juliet despite his reservations?

The first
reason thatagrees to marry the two young lovers, despite his worries, is, as stated above, that
he sees it as a way to reconcile the warring houses of Montague and Capulet. He states this
clearly and explicitly in the following lines:

In one
respect Ill thy assistant be,

For this alliance may so happy prove

To turn your households rancor to pure love.

There may be other reasons lurking in the back of his mind that are not stated
explicitly. 

Friar Laurence is a Roman Catholic monk and priest. As such, he
would have a duty to prevent his young charge from committing the sin of fornication.is rather
obviously a young man who is quite tempted by this sin. Friar Laurence therefore might have in
mind the dictum of St. Paul:

I say therefore to the
unmarried and widows, it is good for them if they abide even as I [i.e. be celibate].  But if
they cannot contain, let them marry: for it is better to marry than to burn. (1 Cor
7.8-9)

Thus he may feel that if Romeo settles down and
marries, he andwill be less likely to have sex out of wedlock, which would endanger their
souls.