Alphard wants to kill the complete version of Canaan. Right now, Canaan is supposedly incomplete, and the despair she will feel after Maria dies will allow her to reach her maximum state, like Alphard has already reached hers. That is the same reason why Alphard killed Siam.

Alphard probably believes it is meaningless to defeat Canaan before she reaches her peak, since that would not release her (Alphard) from her despair. Part of her despair is in knowing that she has reached her limit, and that there is someone who can supposedly overcome that given time and the right catalyst.