Here's a guess: There's a strong sense of organizational rivalry, bordering on hostility, between the Java and .Net teams. If that weren't the case, I'm pretty sure you'd simply promote the head of the Java team to become the head of the combined departments, especially if she has the ability you describe. The most likely reason you aren't thinking along these lines is that it would create the impression of a hostile takeover of one team by the other.
You can go one of two routes:
- Promote the manager anyway; establish team leads for the .Net and Java teams to report to her, and don't worry about the rest. She'll figure out how to make the interpersonals work.
- Figuring the current organizational structure is working well for you, don't change it. You have a year or so to recruit or develop a replacement. Take advantage of having the time, and do so.
The disadvantage to the former approach is that it adds a management layer, increasing the organizational distance between you and staff-level employees. The disadvantage to the latter: If the manager who is staying is ready for and deserves a promotion, this is an opportunity to provide it.
Either of these two alternatives can work just fine, or they can fail. The outcome depends mostly on who sits in each of the critical chairs.
This story, "Your company reorganization: Keep it simple, stupid," was originally published at InfoWorld.com. Read more of Bob Lewis's Advice Line blog on InfoWorld.com.