I would love to see Signal provided on F-Droid, as I mentioned above, but I would temper my criticism quite a lot more than yours, for a number of reasons:
1. I haven't read/heard excuses based on updates/features/metrics/&c. as you mention, but their one performance excuse sounds reasonably plausible. Moxie has commented that he'd welcome a PR[0] even if it had bad performance (provided it only ran conditionally of course).
2. The tone in your Github link is a bit heavy-handed, and calling it malware is going too far, but I can understand the developer of software for which security is extremely critical advising strongly against using an outdated version that's being built and distributed by someone else. There is definitely no implication in that comment that F-Droid is malware, he's only referring to TextSecure.
3. I understand your Github link was just to provide an indication of Moxie's tone, but it is very old and the actual factual details in there are probably not very relevant today.
4. I trust the F-Droid software itself, but not necessarily the repository. The distribution of the outdated TextSecure above is as good an example as any - the idea of a 3rd-party building TextSecure and providing it through F-Droid may be all well and good in the spirit of Free Software, but it doesn't really instill trust when the actual author of the software isn't involved at all.
Finally, I'd never heard of the Gandi issues with Moxie's cert before reading that article. After reading it, I'm much more inclined to be suspicious of Gandi than of Moxie. The article is littered with red flags - that fact that their initial response seems to be to go after their customer rather than to question their business relationship with Comodo being a big one.
[0] https://news.ycombinator.com/item?id=12883410