MechAssault isn't canon, in fact it's as anti-canon as possible so don't take the WoB from that game as gospel. Fun as hell and I wish we got another one so we'd have 3 different types of Battletech games (BT, MW, MA) though. I think we talked about it a while ago but I'm too lazy to search for them, the Jihad itself wasn't the worst thing ever but the fact that it led up to the ever-hated Dark Ages certainly helps sully its image.
As to why Dark Ages is so hated that people shit on the Jihad by proxy, one of the big issues was because FASA (I think, hope I'm not mixing up companies) was facing a crisis of sorts, so rather than die completely they simply ceased operation and proceeded to license Battletech and other IPs out. This was around the FedCom war, also known as peak BT, IIRC. I don't recall the details but the setting jumped pretty far ahead, the writers were told to "figure it out" while also on a time crunch, which culminated in some of the worst decisions imaginable. Like, whoever was in charge of writing this shit was the worst people to have on a time crunch.
Writing quality dropped hard, beloved characters were butchered or killed unceremoniously (not even off screen, barely a paragraph dedicated to them before swiftly moving on), random factions propping up with no build up and probably to die immediately, it's basically the End-Times of Battletech. This also affected the Jihad I believe since later on another company tried to unfuck it, which pleased nobody and fucked the timeline even more. It was just a big mess. Someone could probably explain it better than I can but that's the gist of it.