If your concern is the downtime of the big3d agent while it's being updated during F5 device discovery, then probably the manual update of the big3d agent would be the recommended way. For the active / standby configuration, as you correctly pointed out, you would update the standby device first and then fail-over, and again update the big3d on the standby device. Here's the article describing the manual update of the big3d agent: http://devcentral.f5.com/wiki/default.aspx/MgmtPack/Big3dManualUpdate.html.
I think the risk of config changes related to servers being removed from pools during the big3d update is close to none, if you the manual update of the big3d agent. You can always sync the config from the active to the standby, prior to fail-over, and then your config is up-to-date when you'll do the big3d update on the standby again.
Let us know if you need further assistance for manually updating the big3d agent.
Julian
F5 Management Pack Team
Nimbostratus