This is the sort of enquiry we expect to be dealing with over the next few months!
As all your training for the NPPL(SEP) will ultimately count towards a JAR-FCL PPL(SEP), just go ahead and train the student with his/her NPPL medical declaration. It is only the licence privileges which are affected by the medical held by the applicant. But the medical declaration is a matter between the applicant and his own GP - not with some old quack who'll sign anything for a couple of beers!
If the applicant can't (or doesn't want to) obtain a JAR Class 2 medical, he/she will be able to exercise the NPPL privileges within the limits of the NPPL medical declaration held.
We will be working with the CAA to define the 'upgrade' route from NPPL(SEP) to JAR-FCL PPL(SEP) once the initial NPPL work is concluded; the CAA have stated that they will agree the level of accreditation as well as the upgrade training and testing required.
So it should be possible for a student to start with gliding, then perhaps microlighting, get a NPPL(Microlight), then add the NPPL SEP rating and then upgrade to JAR-FCL PPL assuming the medical is OK.