Tier 4 -> spouse visa

My partner is from Montenegro and is nearing the end of her Tier 4 student visa. We are thinking of trying to get a spouse visa, but wonder what the best way forward is, and what we would have to do. The relevant information is:

- I am a UK citizen
- Been together for 6 years
- Lived together cumulatively for about a year and a half in two different addresses with gaps in between, due to being long distance for a period of time, and a period of difficulty in our relationship
- We currently live apart
- She has studied at undergraduate and PhD level in UK universities
- I have been earning £45,000 for more than 6 months
- She earns around £18,000 as a stipend
- She should finish her PhD this year, around September

My main question is, given our current situation do we have to get married for a spouse visa? I believe the main purpose of the marriage is to prove you are in a serious relationship. Also if we need to be married am I correct in thinking this needs to be approved by the foreign office as well?