20 years is a bad comparison point for "did Disney kill Indiana Jones." Disney bought Lucas just over 11 years ago. So what was the shape of the franchise at that point?
After a well-received film in 1989 and a well-received but niche Fate of Atlantis video game in 1992, and a TV series for a year or so (so not a smashing success, though I remember people liking it) in 1992-1993) it went dark movies/TV-wise, and none of the followup video games amounted to too much.
So the franchise wasn't in great shape or popular relevance pre-Crystal Skull, and that film certainly didn't help. It was largely disliked by audiences, and Dial of Destiny actually seems better received by audiences so far. Personally I thought it was a far better film, though not a "must see" - but how much blood is in that stone to squeeze out with an aging Harrison Ford compared to, say, Uncharted?
Anyone blaming Disney for the state of Lucasfilm franchises seems to have a huge chunk of selective memory for the 2000s. (E.g. for me, I stopped paying attention to a lot of new Star Wars media for a while after Vector Prime in 1999 and the resulting story arc.)