The scale and the fuzzy boundaries between products and services that software allows seem to create those problems in unexpected places. In the pre-software days, if you sell cash registers to people and one of your customers happens to be evil no one would blame you. If you build an online shopping platform (selling virtual cash registers), get big enough that people notice you, and one of your customers is problematic in the eye of the public opinion, you suddenly have a moral problem on your hands.
There are plenty of jobs available that don't involve moral compromises (beyond those inherent to existing) if you don't go out trying to create them.
If my employer buys wood and converts them into staircases, we make a good quality product at a fair price, our working practices are safe, and our suppliers, workers and customers are all working with us by choice - whence comes the moral compromise?
If I'm a surgeon fixing broken arms in a country with single-payer healthcare, I'm doing my job competently, and I'm not getting anyone addicted to pain meds - isn't everyone better off for me having done my job?
If I'm a gardener and I make people's houses look nice, as long as nobody's hiring me to bury human bodies, once again, what's the problem?
For readers who want a job that doesn't require you to shelve your morality, there are options out there :)