Actually, the character on 'Bones' does spell it with an A (I triple checked since I've been using it in fan fiction for years!) per this website by Fox: http://www.fox.com/bones/about/
Also: In the T.V. show "Bones", Temperence Brennen is spelled "ence" rather than the dictionary correct "ance". This does not change the pronunciation of the name, and is, perhaps, more visually appealing as spelled this way, both names only have "e" as a vowel.
There is a brilliant character called Temperance Brennan in Kathy Reich's graphic novels now made into the new series Bones staring Angel's David Boreanaz.
SlayerKat, actress Emily Deschanel is portraying Temperance Brennan. I just thought I'd mention that, now that you mentioned David Boreanaz, who portrays Seeley Booth.