I think you're right that it started out as a short term gain situation. However, Monsanto has been around a long time (they're responsible for DDT, Agent Orange, being in charge of the Manhattan Project and responsible for the Texas City Disaster all the way back in 1947). Companies don't last as long as they have without long term strategies.
If they see that their product is having a particular negative effect (ruining people's health), then business-wise, what is the move that will make the most money? Is it to own up to the problem and pay for clean up and reparations? That's the right thing to do, but they will never do it. They didn't do it for the 500,000 Vietnamese people killed or born severely deformed by Agent Orange, or the American veterans whose health has been ruined by the exposure or their children who suffer from the effects of their father's exposure.
What will make the most money is:
1. Denying there's an problem
2. Calling everyone who insists there's a problem crazy, delusional, or a conspiracy theorist
3. Paying money to stop studies being done that would prove your product is unsafe, and paying money to have your own slanted studies done.
4. See who profits from the problem and invest in them to make even MORE money. In this case, the pharmaceutical industry profits from people getting sick, so they invested in them. Now they have a vested interest in making/keeping people sick.
It's not that far of a stretch, and not out of line at all with their past actions and business strategies. Their executives are deeply entrenched in our government to the point now where they've gotten legal immunity for a lot of things, which is just wrong on so many levels.