Not allowing research use would be entirely antithetical to the patent system itself.
[This post is my opinion, not legal advice, and is provided for entertainment purposes only.]
Note that everything you "invent" that builds on the prior patent, including what you publish, is still blocked by that patent. And even if you ultimately remove the patented part, they can claim it was needed in the research process. So wantonly infringing on a patent in your research doesn't hurt the patent holder anyway.
For businesses, it's still a big deal most of the time because you usually can't really neglect the US market, but for academia, there is no such issues.
That is sadly untrue. There is a lot of confusion on this front because "software patents" are a specialized term of art that essentially means 'a patent that describes a procedure with no reference to a machine'. There was a period of time in the US when such patents were enforceable, but more recent cases have mostly changed that (Basically Diamond v Diehr in 1981 to CLS v Alice in 2014).
But all this is moot, because patents that apply to the software-implemented functionality of machines are common even without "software patents". I've followed more patents on software cases in _germany_ than anywhere else.
You're absolutely right about businesses. The US alone would be enough of a problem, but it isn't even the US alone that is an issue here.
Essentially all software patents describe the von Neumann architecture and make sure to reference machines for this exact reason. Even when it runs on commodity PCs, the patent will still take a ridiculous amount of space to discuss how the RAM is attached to the CPU etc.
I don't know if the patent was ever enforce, but I know for a fact that some companies intentionally adopted SURF and variants derived from SURF due to the patent threat.
As an undergraduate I worked as an RA for some (IEEE published) research at my uni for some robotics work and I gather that violating the SIFT patent was somewhat common when it wasn't obvious SIFT was being used, e.g. when SIFT was being used as a fungible solution:
Self-driving car demo that recognizes road-signs? No, that's too obvious.
Object recognition primarily using HOG or other approaches but using SIFT as a fallback or for determining a confidence value? Go ahead.
And SIFT was used in a lot of private projects (proof-of-concepts, etc) or lab workers' weekend personal projects. This was in academia, but I'm curious if this attitude extends to industry anywhere.