System message is when the account was deleted due to inactivity (by server). Deleted is when the account is deleted by the player (with the account deletion option).
I just tested it. The recipient deleted the telegram I sent and on my side still appears normal, does not appear "deleted" in the recipient's stead.System message is when the account is deleted, either manually by the player or for inactivity. Deleted is when the telegram is deleted by the recipient.