NoScript's behavior isn't the display of ads though, so AdBlock is _not_ directly messing with NoScript.
It could be that the users installed AdBlock to block the NoScript ads. In this case, NoScript is giving the finger to the users opinion.
At some point when the default behavior of two programs with similar feature-sets overlaps you just have to leave resolving them as an exercise for the user.
But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas, but if one of them silently disables or cripples the other on purpose... who is in the wrong?
One of the big points in that article mirrors your example. The correct response is to allow the user to decide.
"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas"
"This software program conflicts with this software program. You can choose to run them both and accept the problems that occur accordingly or you can choose to cancel this installation or remove program X"
Do you want to cancel, remove program X, or cancel the installation?
Give users the option to opt-into using your software, don't force users to get into a proxy battle by automatically opting into things.
"But targeting the other program in such a way is no different than someone installing two A/V softwares. Sure they may conflict in some areas..."
No. Hell no. Antivirus programs conflict for a good technical reason. NoScript and AdBlock conflict because the author of one dislikes the effects of the other program; were it not for that, the two extensions would be completely compatible with one another. Equating these two things with each other completely misses the point.
I'm giving an example of a way to approach this problem. Installing Noscript could add a rule to an Adblock whitelist. What Noscript is doing by trying to sneak it in is wrong. If they wanted to overwrite a rule, let the user do it. As that article points out, and as Mozilla points out, making that the non-default option is very important.
Part of NoScripts behaviour is the display of it's ads.
That's what it does - it displays ads as part of its website on the extension update page. So those ads are part of the extensions behavior.
Obviously some users supported the NoScript author through the ads or donations. So by blocking those - and blocking the update alltogether - AdBlock was disrespecting what some of the NoScript users wanted.
My point still holds that both were not doing the best in the interest of their users, mozilla, or even themselves.
Both are doing wrong in a way... but not in others. It's a contradiction, but neither can claim to be the white knights... both are at best grey.