I do think the problems for students will come further down the line, rather than say, at the university application stage. Also, problems will be greater for those who miss out on C grades, rather than A* grades (although this could be equally personally upsetting).
I've dealt with admissions at a fairly average university. For the school I worked in, certain GCSEs were required- at least a C grade in maths and English and a C or a B grade in biology or double science depending on the course. Beyond this, actual GCSEs weren't looked at too much (although we did have access to AS grades). When most of this cohort apply, it will be remembered that they had a more difficult year WRT GCSEs than others, and they will be mainly competing with each other for places. However, the C grades for maths and English won't be an area where compromise is made, as it's likely the courses could easily be filled without bending this requirement.
The issue will come in 5 or 6 years time, when people might consider returning to education, but the particular issues this year will have been forgotten. For example in 2008 (?) the A-level syllabus for many subjects changed in order to phase out cw- the students who took the first exams in the new syllabus were probably at a disadvantage. At the time, this might have been known to people in admissions and maybe taken into account, but now it has mostly been forgotten about.
Universities and colleges at least pay attention to exam changes, but most employers won't. When filtering job applications, it's easy just to reject those CVs without 5 A-C grades or whatever the minimum you want is. The year the applicant took the exams may not even be noted, let alone taken into account. Most employers won't remember that 2014 was a bad year to take your GCSEs in a few years time. They'll just compare grades as if they are like for like.
This isn't meant to be doom mongering, but I do think it's a serious issue and children's futures shouldn't be used as political football.