日本に帰るのは大丈夫ですよ。心配なら一応確認した方がいいかもしれませんが。
ビザ延長のガイドに↓のように書いてあります。
May I leave Canada before my request for an extension has been finalized?
Yes. However, if you leave temporarily and you do not have your new document before you seek to re-enter Canada, you will have to re-apply (either at the port of entry if you have the right to do so, or at a visa office outside Canada) and pay another processing fee.
http://www.cic.gc.ca/english/pdf/kits/guides/5551E.PDF、p.6