You need a new kernel, yes, but there's no flashing required

ubiboot is a boot loader, it loads your selected kernel from a file in userspace filesystem to memory and boots it.
That's the reason it can boot many OS'es, each with up to 6 selectable kernels. (there's the README document that tells you some things on how it works...)

Now, what you do, is you just copy the kernel image that's suitable for Nitdroid into /boot/ directory of your Harmattan installation, the same place that you now have your L2-fixed kernel, and then you write up a configuration entry for it in your ubiboot.conf file.

That's it. No flashing required, never again