I'm pretty sure that the only way eligibility is lost is when a player actually plays in a game, fall or spring. So if this player attended school in the fall, and did not play fall baseball in an actual game, then he still has 2 years left of eligibility.
As far as seniors not being drafted as high, this isn't entirely true. The reason you don't see many seniors in the the 1st 5 rounds of the draft is because all of the top players come out as juniors because this is where the money is for college baseball players. Seniors are seen as easy signs and receive significantly less money than juniors (except in special cases). So the question is, if this LHP is good enough, he'll get drafted where he should get drafted, but he would have a better chance of getting a good signing bonus as a junior.
Now, I'm also pretty sure that MLB did away with the entire Draft and Follow process this past year. That means that the team that drafted this pitcher does not own his rights. Also in that mix is the fact that he did attend a 4 year college, so he is now fair game in next year's draft. Also, I don't think he can sign a pro contract until next year's draft as well.