Subordinate milestones are always rolled up into the parent task when rollup is used.
Perhaps a better way of representing what you need might be to use the Timeline functionality. Go to the View menu and check the Timeline box. Then you can mark individual tasks and milestones to be represented in the Timeline at your discretion. These are not affected by rollups.
Another common method, if you don't use Timeline, would be to create key milestones at the top level and link them to the lower level milestones. Since these are not subordinate they would never be rolled up. I use these a lot to represent things like "Development Start", "Development End", "Testing Start" etc. etc., in conjunction with adding the task dates to the Milestone bar style, so that a rolled up plan clearly shows the major milestones- I often embed that within high level project progress reports.