Update:
1. I found my contract. It is very specific about what things you can and cannot keep within the property. There is no mention of bicycles.
2. I have now received a letter from my agency stating that I am not allowed to keep bicycles in the property so as to avoid marks and damage.
3. My flatmates BSO, also kept outside the property like my now stolen cheap bike, was stolen last week.
4. My insurance does not cover any bikes that are not kept behind locked doors within the property.
5. We are on a rolling month by month contract, so the agency could decide to terminate the contract at any time with 4 weeks notice.
6. We have a legal advice line given to us at work. I shall be making use of it on Monday.
7. We pay a combined rent of £700 per month - I don't think any possible cleaning work or minor repainting to remove any currently non-existent marks on the property would be worth losing even one month of rent for the agency or landlord.
8. My flatmate, whilst he has been helpful advising me, wants no part of this and doesn't want any negative effects on himself.
9. I think my best course of action will be to write a letter to my agency, stating I am sorry for these issues coming up, stating my bikes whilst they have caused marks have caused no damage and any marks are easily cleaned off, and I am happy to take responsibility for this. However they must understand my bikes are my main means of transport, that I simply cannot keep them anywhere else, especially as it is not secure (nor insured) to keep them outside, and that I am not in breach of my contract by keeping them. I am however happy to come to some kind of mutually amicable compromise should one be possible - but if they are insistent the bikes go, then I will have to go also.