Is this sentence fine?
He gave his opinion on this issue. I’m more against it than for it.
Or what else can I say expressing the same meaning?
"I'm more for it than against it" sounds a lot better to me than the opposite. The most succinct way to say the same thing might just be simply:
He gave his opinion on this issue. I'm inclined to disagree with it.
(or "with him").
It conveys both that you don't agree, but also that it's not a 100% disagreement, and flows more smoothly than your example.
As long as the antecedent is clear, there is no harm in substituting a pronoun for a subject. In this case it is clear that it refers to "his opinion" on the matter. So, yes, it's fine as it stands.
You could say things like:
On the whole, I feel that the bad outweighs the good.
While the proposal has some interesting points, it also has problems that prevent me from endorsing it in its current form.
Certain things will need to be addressed before we can move forward with it.
There are more things that I don't like about it than things that I do like.
I think it will do more harm than good.