I dunno, but my alliance consists of at least 500+ people and the merc corp has about 20 people, maybe.
:I
They are just looking for random war targets then, or someone specific in your alliance. Fly with a couple other guys with eyes on local and you're fine.
If your alliance is bothered by their dec and decides to try and fight them off, it simply won't work and they will have lots of fun picking off your ships indefinitely. If you need to move anything worth a damn then fly with a scout and you're 99% safe.
I've been in high command of 2 merc alliances, and have been charged with moving several billion isk worth of goods through enemy sec with hundreds to thousands of wt's flying about, it all works the same and it's easy to avoid fights with war targets if you don't want to fight.
Just don't be stupid enough to get trapped in a station.