>> So, two questions... can you permanently damage the muscle and bone through not stopping for injury,
You can but it is more likely that failing to rest will simply make the injury last longer. You need to find out if you have an underlying problem or if this is an overuse problem.
>> and also what cardio exercise can I do while resting it?
You could try spinning, body pump, aqua aerobics, cross trainer - your physio can give you guidance here.
I did Portland and Gower last year and they were great but really tough. For Portland save some energy for the beach as that really sapped my energy - I can't imagine doing it twice for the marathon!