We're enountering similar issues. Here's what we've done.
Assign all issues in a sprint to the appropriate fixversion
Go to the Classic Board for the project(s) associated with those versions. Update the start and end date for the applicable versions there (that is the only place these attributes exist). Configure the classic board for the project(s) to map the statuses to the appropriate To Do, In Progress, and Done columns.
Then, use the Agile Gadget and set it up for the applicable project. That way, you can use it to show burn up, burn down, and story points by version.
If Greenhopper added these attributes to the JIRA version management and created an admin UI to map statuses to To Do, In Progress, and Done, then these gadgets can still work without the classic boards. I don't see harm in giving users the ability to configure the statuses for a version in order to use the stop light progress bar as it doesn't have to match columns and status mapping in rapid boards. Plus, you cannot use Greenhopper without Jira; adding these attributes to JIRA version management only makes it easier to have the configuration all in one location and this information is value add to JIRA only users as well - what was the start, end, and release dates for a version. If JIRA folks wanted, they could use the same status mappings for their roadmap gadget. So, instead of showing just red and green, this gives them the ability to show red, yellow, green - thus, users of both products benefit.
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