Step one is to look at the short and medium term answers that I described in the blog post on the topic.
I've asked Nick Hopper, a professor from Minnesota who is taking his sabbatical to work on Tor research problems, to think about the problem more deeply and see if there are good longer-term answers. Below are some of the ideas I suggested that he/we ...
One could advocate crowd-founding a "Tor botnet defense fund". Then pay the most skilled hackers to analyze the malware, find a vulnerability in the botnet, cooperate with authorities and take over the botnet and shut it down. De-anonymize the botnet owner as a bonus.
The issue comes from a lower level. A level, The Tor Project isn't responsible for. One ...
There isn't really a way to stop the botnet entirely. Due to the very nature of Tor making it hard to stop the internal traffic, or identify its source, there is very little that can be done without introducing larger protocol changes.
I'm unaware of any efforts to investigate such changes.
It might work. Tor transports TCP and as you can do OpenVPN over TCP, you can do OpenVPN over Tor.
Other places document how to bond two tun devices, for instance openvpn bond 2 tap tunnels on stackoverflow.
So, while it could work, I'm not sure if it's worth the trouble and network overhead. Probably depends on what you want from your VPN.
I don't know ...