You should be fine, just using the Tourist Visa Exemption twice, although I always recommend getting a visa.

Your Wife should be able to get a re-entry (single re-entry) permit at Thai Immigration, at the airport, prior to flying from BKK to Siem Riep. Leave some extra time to get this at the airport.

This will "preserve" her original 30 day (single-entry Tourist visa) entry stamp.

You'll need a couple of photos, a completed TM.8 form, and 1,000 baht (for a single re-entry).

http://www.immigration.go.th/nov2004...?page=download

http://www.thaivisa.com/forum/topic/...entry-permits/

http://bangkok.immigration.go.th/en/...?page=re-entry