Okay, here's the thing.
(SPOILER)The original game may have started with that premise, but it never really went there after Midgar with the exception of Cait Sith calling out Barret once in Disk 2. Considering we're dealing with a party that was otherwise law abiding and heroic for the rest of the game. It just never felt right that such an edgy opening never panned out. So I'm not surprised that SE is going to keep their record a little more squeaky clean, even if this means we'll now be dealing with the FF equivalent of "Han shot first" nonsense.
The other issue at play here is that SE just won't go there. They may occasionally kill a character here and there, but they tend to stay clear of heavy handed subject matter and VII easily has the most elements in the series. It makes sense to me that SE would choose to make Avalanche (thank god I don't have to capitalize all of it anymore) a softer brand.
The last issue at play here is that the sequence falls closer to a bit more realism. A bomb of that size could never take down a reactor realistically. Especially if Jessie only made it based off instructions she got off the web. They would have either needed multiple bombs placed in structurally sensitive areas or they made a bomb with some more pop, which I doubt Barret's meager outfit could get their hands on and would likely be the size of a truck. The funny thing was that I was actually thinking about this when I reached that point in the plot and was amused when the bomb that went off did minor damage.
Of anything, the new element simply makes new players know exactly what they are dealing with. I was curious to know if SE planned on making the top brass of Shin-Ra less cartoonish, but that moment showed me we'll still be dealing with out usual puppy kicking, mustache twirling villains we all know and love. They just decided to play their hand earlier.