I've got an NL team in Sioux Falls, and we're just getting a new season of games underway. I just tried to set my lineup so that I would have my pitcher hitting 8th and an OBP guy 9th so that the top of my lineup will occasionally have guys on base for them. When I set the OBP guy's place in the lineup without a DH at 9 I get the "there are multiple players at one spot in the batting order" message, but when I set him as 8th, the lineup is accepted. This tells me that WIS automatically programs the pitcher to hit 9th...is there a way I can avoid it ?

Sounds like a bug.  It should let you do it.

I regularly bat my pitcher leadoff in spring training games in NL parks by leaving the 1 slot open in the lineup.

Yeah, I just did it with one of my teams.

I have figured out what happened: I tried to apply the strategy to all the lineups, rather than just the ones without the DH, so in those lineups the DH and OBP guy were listed in the same spot.