Here is a artillery "drill" I do to minimize (not completely eliminate) friendly fire:

Standing fast -
1. Always have roundshot selected.
2. Always limbered.
3. Always have fire at will off (for immovable artillery).

To fire -
1. Unlimber.
2. Click off fire at will.
3. Select ordnance (roundshot should always be selected before you pick your shot type).
4. Select target.

To cease fire -
1. Wait until all artillery have just discharged their latest shot (recommended)
2. Re-select roundshot.
3. Click halt.
4. Wait 1 second.
5. Click limber.

By always having roundshot on whenever you cease fire minimizes your casualties when your artillery starts to turn sideways and shooting down your line (unhappily there is a chance that a roundshot will go EXACTLY down your line and wipe out 20-30+ men; however this is far more preferable to the other types of shot).

The only way to stop the firing sequence animation is to limber. If you did not click "halt", or click limber too fast after "halt", some of your artillery may not limber up. If you did not click "halt" when this happens, be prepared to take a raking volley down your line. Same thing if you limber too slow.