Pitchers throw harder and for fewer innings for the same reason that even the world record holder in the 400m dash can't beat a good high school team's 4x100m time
Maxing out on velocity, followed by waves of relief pitchers doing the same, coupled with everyone throwing breaking pitches designed in a lab, has proven to be more effective than relying on one workhorse to go the full nine.
And this isn't a new phenomenon. While the rate has increased a little more quickly recently, the average number of pitchers used in a game has grown fairly steadily over time (as shown here).
In 1901 the average was barely over 1 per game. It crossed 2 per game in 1946, 3 per game in 1990, 4 per game in 2015. It peaked in 2020/2021 at over 4.4, but they put the reigns on that with the 3 batter rule and it has settled back to 4.28 per game this year.
So yeah, pitchers don't go as long as they used to. They also used to have a dead ball, face lineups where half the hitters struggled to hit the ball out of the infield, and play in parks with dimensions so deep they'd have things like bullpens and monuments in fair territory. Pitcher usage has evolved as the game has evolved. This isn't new.
And it's not like heavier reliance on more relievers had handicapped run prevention. Removing the steroid era and the parts of the 19th century where they were playing pseudo-fastpitch softball with no fielders' gloves, the era with the highest runs per game was the 1930s, when the average pitchers per game was still less than 2 and teams hadn't yet caught on that fresh relief pitchers are more effective than tired starters. Historically, we are in a below-average run-scoring environment.
Having said that, I intentionally used the term "more effective" instead of "better". Some of the romance of baseball gets lost with this more efficient but less aesthetically pleasing approach. It's part of the dichotomy of analytics. Its use has increased effectiveness in all sports. But while in other sports it has made games more exciting (more passing, more going for it on 4th down, more going for two in football), it has arguably made the game more boring (three true outcomes, less small ball, the parade of interchangeable relievers). But the genie is out of the bottle. You can't make a rule telling pitchers "don't throw so hard." It would take extreme measures like limiting pitching staffs to 10 pitchers or requiring a starter to throw x pitches/innings/batters before a reliever can come in (must be replaced by a position player or lose your DH or something equally insane until the benchmark is reached). The chances of any of those things happening are nil.
I don't know how to fix it, and I'm pretty sure baseball doesn't know how to fix it either.