It wasn't just because of that - Themely's developer started to act strange and was deemed untrustworthy by the guide and most members of the community, so when he announced that the newest version of his homebrew theming tool was closed source, people started being skeptical.
If you want to hear what happened, long story short, afterwards it was discovered that unbanmii uploaded your 3DS's private seeds (even if it was an involuntary thing according to its developer), Erman said that it was actually, quote, "quite smart" just as he announced that the homebrew would become closed source. That, along with him distancing himself from GBATemp after being banned for using a racial slur, stopping support for his app on the github tracker as well as on other websites and obstructing users from scraping themes from his websites right after the drama (which also disabled the QR code support function), was basically the last nail in the coffin. Of course, this is a REALLY small recap of all the drama that blew up during that time, so if you want a more personal point of view I suggest you start googling to get a better picture of what happened.
Of coruse, that doesn't mean that you must stop using Themely right now - there are also
open source forks that spawned right before the tool became closed source. The only unsupported and untrustworthy version out there is Erman's own for the reasons I listed above.