Hi,
The seton allows any infection to drain. If it were removed the chances of developing an abscess increase. With an abscess there is likely to be increased pain and possibility that your girlfriend could become seriously ill.
As for surgery, it really depends how much of the sphincter muscle is involved. The usual surgery is just to cut through the fistula and leave it open to heal from the inside out. If too much of the sphincter muscle is cut then your girlfriend could end-up being incontinent.
You don't say if your girlfriend has been diagnosed with Crohn's? If she has Crohn's, the best course of treatment seems to be a combination of surgical drainage I.E. the seton and immunosupressive or anti-TNF drug treatment.
Take a look at this fact sheet from Crohn's and Colitis UK for further information.
http://www.nacc.org.uk/downloads/factsheets/fistula.pdf
Hope that helps and that your girlfriend's situation improves soon.
Regards,
Mark