No, you can't lock it. But it will degrade faster if someone isn't on it, so someone grabbing a quit shot may be doing you a favor, provided they don't stay on it.
When people camp your siege and don't get off, I find /say can I please have my ballista back
usually works perfectly.
Siege was probably intended to stay manned, but good players learned how to set up several siege at once. So, the only way to protect your siege is probably to place one and man it.