I thought I might be having a mold issue in my basement but the quote below seems to describe my issue. My question: This seems to really pit the block. I'm concerned that it will eventually cause the block to deteriorate. I've taken steps to fix the water issue and the basement has been dry for two - three years. Should I be concerned? What should I do to fix this for good? I'm wanting to finish the basement including applying drywall. Will I end up regretting this?

Is the "mold" on the cinder block white? If so you don't have mold you have efflourescents. This is lime within the block that is pushed through the block pores from moisture. If you were to scrape off the "mold" with your fingers it will have a chaulky feel to it. You can scrape this off with a broom and then use Drylock to help seal the blocks.
One thing you need to try to do is prevent the water/moisture from entering the block. It is common to see the efflourescents in the corners of the foundations where there is poor gutter drainage or where porches/patios join the house and the water just sits against the foundation the seeps into the block.

Etch with Drylock etch or muratic acid (dilute hydrochloric) both available at a hardware store, then paint with Drylock paint.

The ETCH STEP is VERY IMPORANT.