It's too bad you are leaving, I really enjoyed working with you.
It's a shame you're leaving the company, especially since we just got to know each other.
この場合、次のように言うと良いと思います。
ーIt's too bad you are leaving, I really enjoyed working with you.
「あなたが辞めてしまうのは残念です。あなたと一緒に働くのはとても楽しかったのに」
It's too bad ... で「残念です」
to leave で「去る・辞める」
to enjoy working with you で「あなたと一緒に働くことを楽しむ」
ーIt's a shame you're leaving the company, especially since we just got to know each other.
「あなたが会社を辞めるのは残念です、特に知り合いになれたところだったので」
It's a shame ... で「…で残念です」
to leave the company で「会社を辞める」
to get to know each other で「お互いを知り合う」
ご参考まで！
カナダ 
