Here are a few ideas to help you keep or recreate some feel in your programming. In other words, if it sounds okay, it is okay. Even when they try to, even the greatest musicians can't play every note exactly in time. Create a repeating drum-pattern to use as a metronome instead of the infernal bleep. Regard dropping the tempo when recording as a last resort.
Velocities Note velocities are as much an important part of feel as timing.
Accent the wrong notes and the beat starts to 'drag'. As a rough guide, assign higher velocity values to the most significant notes. Construction Try to record longer 'live' phrases to get a feel going - constantly recording two bars then stopping prevents you 'getting into it'. If the copies aren't varied in any way, this can give an effect similar to quantizing. Once the second section is up to scratch, spend some time creating a seamless join between the two sections to disguise the fact that they weren't recorded as a continuous whole.