Friar Laurence certainly has some very mixed emotions concerning Romeo and Juliet's marriage, and if he were chronicling his thoughts after conducting the ceremony, he would certainly mention both sides of his emotional state.
We see the first way he feels about the marriage in Act 2, Scene 3. After Romeo informs him that he has so suddenly switched from being in love with Rosaline to being in love with Juliet and that he wants to marry her, Friar Laurence responds by saying that the marriage could be a good idea for the two warring families. His primary concern is to put an end to the violence caused by the two families' feud. He feels that a union through marriage will give the two families an excuse to finally set aside their differences and establish peace, as we see in his lines:
In one respect I'll thy assistant be;
For this alliance may so happy prove
To turn your households' rancour to pure love. (II.iii.93-95)
However, in general, Friar Laurence thinks the marriage is a far too hasty idea, especially because he sees Romeo as being too young to truly know what real love is. Romeo is confusing real love for sexual passion or infatuation, leading to his fickleness. We see Friar Laurence rightly associate Romeo's fickleness with his youthful naivete in understanding real love when he says, "Young men's love then lies / Not truly in their hearts, but in their eyes" (69-70). In addition, he argues that Rosaline was very wise to reject his love and says it was because she saw his love was far too young.
Since Friar Laurence sees that both Romeo and Juliet are far too young to really know what love is, he also feels that the marriage, though it may help the two families, is an imprudent idea. We see Friar Laurence expressing his hesitations just before he marries the couple in Act 2, Scene 6 when he hopes out loud that "heaven" will not later "chide" them for this "holy act," meaning punish them for such an imprudent idea (II.vi.1-2). Not only that, he prophetically warns Romeo that such "violent delights have violent ends," meaning that their love is not likely to last since it is not the sincerest, truest form of love (9).
Hence, if Friar Laurence were recording his thoughts, he would definitely express both his hopes and his doubts. One way he might start his journal entry is by asking himself, "Did I do rightly, or did I make a mistake?" From there it should be easy to relay all of the mixed emotions we see Friar Laurence expressing in these two scenes of the play.