You (as the parent) could speak to the HOD or principal, to
request that your son be allowed to take the 'O' level A Math
paper, even if the school does not allow him to
attend A Math classes in school (tell the HOD or principal
your son has private tuition for A Math).
If this fails, in the worst case scenario, he
can register as a private candidate, and take A Math
(and Pure Chem or Physics, which will allow him to take H2
Chem or Physics in the JC, which is requried for many Science
courses in the Uni; he can still take H2 Chem or
Physics in the JC if his combined science gets an
A1, but one problem with combined science is that one science
performed badly can pull down the other science).
He can't register as a private candidate in the same year as he
is a school candidate, which means he may have to retake as a
private candidate the year after he leaves the school. He can apply
for one year deferrment from NS, which even if the deferrment is
not granted, he can retake as a private candidate within NS,
or in the year he ORDs (completes NS).
Millenia Institute may not be a prestigious JC, but one good
point about MI, is that it has more flexibility and more merciful
criteria (in terms of O level subject background or
scores) for students to take A Math and H2 Chem or Physics.
And what's more important about being in a prestigious vs
neighbourhood JC, is your son's own hard work and
perseverance.
If your son wants to do Science in the Uni, it's still more
important to do H2 Math and H2 Chem or Physics, either in a
neighbourhood JC or MI or even as a private candidate, than to be
in top JC in Singapore but not have these prerequisite subjects
that the University courses require.
My point being : when there's a will, there's a way. That's the
single most important lesson you need to teach your son.