Mark an LTM virtual down when pool in an irule is down.

I think it really depends on what you mean by "down". If you mean that you don't want to send any traffic to the iRule-referenced pool based on availability of the attached pool, then you could use the active_members command:

https://devcentral.f5.com/wiki/iRules.active_members.ashx

If, however, you need the VIP to be disabled completely, perhaps so that GTM will see it as down, then you could use an iCall (or raw user_alert.conf script) to effectively disable the VIP by triggering TMSH commands on Syslog monitor events.

https://devcentral.f5.com/questions/clearing-machine-cache