You can easily offset that with research. I was afraid of such issues, but in my current test playthrough I was getting constant 500+ score in early months, despite bagging only 1-2 missions monthly and not doing Pogroms.
And yes, you naturally lose for constant negative score/negative money. No point in prologing the agony, is there any?
I'm not sure if the RNG is trolling me or what, but I did every mission available to me in January, completed all but one Ratman Rodeo (I did kill a bunch of them and take loot home), researched a bunch of stuff (which I do recall being worth a lot of points in earlier versions) and even landed at the pogrom and shot a few guys until the tank showed up. I was at around -300 before the pogrom, and after research bonus I was still -250 in the hole at the end of the month. Then something in the first week of February knocked me down to -200 right off the bat.
The charts indicate quite a bit of shipping activity in areas I can't see, but the score penalties seem unusually high. About 95% of shipping that I could see was civilian and never landed. The rest were larges that outran the airbus and went about their business.
I'll reinstall when I get home, maybe I copied the wrong UFO files.
@ivan: I have no option to buy any craft. Maybe that's an issue in and of itself.