Yes. This scheme has been designed to help congregations adapt their buildings to cope with a changing climate, and you can apply for a grant to improve, rather than just repair, rainwater disposal systems. You will need to ensure the works you propose follow good conservation practice and are likely to be approved by the relevant ecclesiastical or statutory permissions authority.
The application guidance says only like-for-like repairs are eligible but our gutters and hoppers can no longer cope with the increase in rainfall. Can we apply for a grant to upgrade them to disperse a greater volume of water more effectively?