We dont have any local CofE secondary schools, but from the Collective Worship policy of a local-ish CofE Voluntary Aided primary school:
We expect all children to attend worship. However, any parent can request permission for their child to be excused from attending religious worship and the school will make alternative arrangements for the supervision of the child during the period concerned. Parents do not have to explain or give reasons for this. This complies with the 1944 Education Act and was restated in the 1988 Education Reform Act.
I'm quoting this school's policy because it details the underlying legislation. Basically, anyone has the right to withdraw their DC from their school's acts of collective worship.
However, another, more local school (same diocese) words their policy along the lines of, Well, you've got the right to withdraw your DC, but we hope you won't, given that you decided to send them here in the first place. And yet another school, again same diocese (in fact, the MAT it belongs to is the 'diocese MAT'), doesn't appear to mention the subject at all.
So yes, you have the legal right to withdraw your DC; in the absence of details in the school's policies re whom to contact (or a published policy at all), I would either drop in at the office, or use the 'contact us' email in the first instance to check how to withdraw officially. Although at the end of the day, if you are fine with however much the school adheres (or doesn't) to the requirement for a 'broadly Christian in nature' daily act of worship and it's only the 2 church services that are the issue, you could just report your DC's absence for the relevant sessions at the time, citing withdrawal from attending the service as the reason?