Well, a bit later in the scene there is this:
Meph. I am a servant to great Lucifer,
And may not follow thee without his leave
No more than he commands must we perform.
Faust. Did not he charge thee to appear to me?
Meph. No, I came hither of mine own accord.
Faust. Did not my conjuring speeches raise thee? Speak.
Meph. That was the cause, but yet
per accidens;
For when we hear one rack the name of God,
Abjure the Scriptures and his Saviour Christ,
We fly in hope to get his glorious soul;
Nor will we come, unless he use such means
Whereby he is in danger to be damn’d:
Therefore the shortest cut for conjuring
Is stoutly to abjure the Trinity,
And pray devoutly to the Prince of Hell.
So maybe the holy water and the sign of the cross (not to mention
"Valeat numen triplex Jehovae!", LOL) actually
were counterproductive, but because he wanted to get Faust's soul, Mephistophilis was determined to appear and so had to work very hard to counteract them.