Honestly, given how many people do work here when they shouldn't, compared to how many people get caught, I wouldn't worry about it.
I'm going to assume your company is a real business making real money (not just something to get you a visa). Some people will say you need a WP to sign company documents, but if that were the case we'd all need WPs to sign any contract (condo, internet, etc). So long as you are no longer spending your time in the office, factory or whatever ordering people around it should all be fine.
Of course getting legal advice is always advisable.
Follow-up: put paperwork in with printouts of flight out of Thailand yesterday, and collected passport after 1:30pm today. They've given me a second back to back single entry non B visa.
There is quite a bit of Thai written on it, perhaps someone in this group can translate.
The girl in the consulate was quite helpful. I even checked with her that *if* I don't put my application in until tomorrow (Wednesday) would they be able to process it in time for me to fly back to Bangkok on Thursday. She said they would.