The Duty of Care which was introduced with the updated animal welfare bill states that it is the responsibility of the owner to ensure that your pet must be kept with, or separate from other individuals as appropriate.
There is nothing to say specificcally rabbits and guinea pigs at this moment in time, and there is basically no way they could be prosecuted under current legislation, because keeping them together has been such common practice and there will still be places recommending it.
However, it will be interesting to see what happens when the individual species Codes of Practice are brought out - the rabbit one is currently under consultation, and it may well state on there that rabbits should not be kept with guinea pigs. But then again, it may not. If it is stated in the COPs, then they may have an obligation to separate them. However, if it is not mentioned, then I suspect there will be no legal action which could be taken.