I shouldn't worry about the GCSE as that is the least likely to be overly religious.
However, it is the KS3 teaching that is more likely to be religious as the school might be classed as a school of a "religious character" (depending on whether it is VA or VC) and so able to do denominational teaching at KS3. However, if you are unhappy with this, you do have the right to withdraw your child from RS. But note, the school does not have to do any other teaching in this time.
At Key Stage 4, RS remains compulsory (with the right to withdraw) but this does not have to be a GCSE course. It doesn't even have to be weekly lessons (could be collapsed timetable days etc) but it does have to be done by law. Any school which does not provide RS at KS4 is breaking the law, but changes in OFSTED etc over recent years has seen more schools do this.
At GCSE, the syllabus is set by the exam board. The overwhelming majority of schools at the moment teach philosophy and ethics, but there are other options that the school can teach. For example, they could teach a gospel (often Mark's) or study Catholic Christianity (there's not a C of E option) or just a study of comparative religion.
However, by the time your daughter does her GCSE the syllabus will have changed and the rules will be different. Under the new spec, philosophy and ethics will make up a much smaller percent of the course (25 - 50%) with students having to study at least two world religions. I was at the recent government consultation on the changes, and a lot of us RS teachers were very unhappy with the spec changes, but these are politically driven and we didn't get to see half the changes we asked for.
And yes, A level RS is viewed as a decent option. Trinity College Cambridge rank it as an A2 subject - the highest category for Arts A levels.