Thanks for this question. I definitely understand where you're coming from.
As the creator of Q2A, I see two issues with licensing it under GPL immediately. First, it means inviting significant user contributions, before I feel the code base is really ready to absorb them. For example there are some major changes coming in 1.0b2, and it would be hard to work on those while other people are working on the code independently.
Second, a GPL-style license would really reduce my future options. I imagine Q2A will always be free for public websites, but I may want to charge in other cases, e.g. for companies who want to use it on their Intranet. If I made the license GPL, I lose almost all control over how Q2A can be used.
That said, I am very open to changing the license in future. I just feel that it's too early to go straight to a full-on open source license.
As for your modifications, it would be really helpful if you'd contact me at Q2A feedback - http://www.question2answer.org/feedback.php
- to let me know what sorts of changes you are working on. I can then integrate these myself, or perhaps put in place an appropriate plug-in mechanism that will keep the interface between Q2A and your code clean, even while Q2A goes through future changes.