Congress has the power to declare a war, which was supposed to prevent the Executive from taking any military action that was not purely defensive, without their approval. There was even a requirement about how long the President had to give an accounting to Congress about any action they did take. So yes, Congress was supposed to have the ability to "command" the military insomuch as they could choose whether the Executive could utilize them or not. Saying "no, you're not going to do that" is an authoritative command.

Hamilton, Washington, and Madison all separately wrote that Section 8's War Declaration clause was intended to be a substantial limit on the President's power. Even the small, mini-conflicts in the 1800s required Congressional approval to initiate, it wasn't until the 1950s that the Executive branch destroyed that check on Executive power.