Quite easy to solve: Use /target to choose what you're sheeping.

Rather than /assist focus, just change the /cast line to:
[code:1]/cast [target=focustarget, harm, nodead] fireball; [target=party1target, harm, nodead] fireball; fireball[/code:1]
This will first attempt to cast a fireball on the target of your focus - WITHOUT targeting it - then attempt to cast a fireball on the target of your party1 - again without actually CHANGING your target - and finally just attempt to cast a fireball.

And your new sheeping macro:
[code:1]/cast [harm, nodead] Polymorph; [target=focustarget, harm, nodead] Polymorph; [target=party1target] Polymorph
/stopmacro [harm, nodead]
/assist focus
/stopmacro [harm, nodead]
/assist party1[/code:1]
If you're targeting something that you can sheep, you'll do it, if not you'll check the target of your focus and party1 - again this is without choosing or changing a target, I usually use these sorta commands to fire slow spells without telling what I'm shooting at, less chance they try to interrupt if my official target is out of my range - before targeting 1 of the 2 (whichever one you can attack).

Really the only difference between Focus and Target is that anything that attacks you while you don't have a Target is made your Target, so this will also let you sheep the attacker of your mage more easily.
And the whole [target=focustarget] making it seem like your alts are blocking the ToT just makes your enemies appear foolish when they report you for cheating. Added benefit. I started doing it with [target=mouseover] when I was still single-boxing and haven't stopped laughing yet :P