Most likely because Leonard had to be alive long enough to instigate Vanya's wrath. The series of events that made Vanya literally explode was:
- Vanya meets Leonard
- Vanya falls in love with Leonard
- Leonard gains Vanya's trust
- Allison attempts to split Vanya and Leonard.
- Vanya slits Allison's throat.
- Leonard and Vanya run away and he tries to convince her to get revenge on her family.
- Vanya gets enraged and murders Leonard.
- Vanya goes to the concert and the apocalypse begins.
So Leonard was vital to Vanya's descent in to madness. The last four steps in particular happened in the span of a few hours which is a lot for someone to handle. If he was murdered by someone else at an earlier point, then Vanya could have potentially been talked back down. Since she was the one that killed him, and since she was the one that felt betrayed by everyone in her life, she was willing to destroy everything.