He watches her reaction, such as it is. He's concerned she can't accurately feel the pain, but on the other hand he doesn't need to hold her still. He's able to finish with patching her up in a timely manner, which is important just in case the blood attracts Beasts. Altaïr doesn't want to compromise everyone on this expedition.

"If he keeps attacking you, then aren't you just continuing to frighten him? Do you know what caused him to be frightened to begin with?"