You should take a look at how Claude Code does its permissioning. It's totally fine to connect it right up to your GitHub MCP server because it'll ask each time

You should take a look at how Claude Code does its permissioning. It's totally fine to connect it right up to your GitHub MCP server because it'll ask each time it wants to take an action (and you can choose "don't ask again for this tool" if it's an obviously safe operation like searching your PRs).