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Had a situation this weekend, runners on 1st and 2nd, 2 outs. Batter hits a ground ball to SS, it would've been a routine 6-3 out, except the runner coming from 2nd was hit by the ball and obstructed the fielders path (ran into him basically, and then got hit with the batted ball). Batter was called on being hit by batted ball...okay, got the out on the runner, easy enough. I did have pause on what to do for the batter, so I scored it as a fielders choice, because it would have been, like I said, a routine 6-3 out. Was this correct for the batter?

Yes, fielder's choice is likely the appropriate choice in that case.

Ok, like I said, that's what I thought, but I had someone question the score...like to take a guess who it was, lol. So I wanted to ask.

I need to check the rules, but the batter who batted the ball which strikes a runner in front of a defensive player is credited with a hit.

Yep, award batter with a hit, runner is out for hit by ball.

I believe it is a fielder's choice if the scorekeeper believes it would have been a routine put-out if not for the interference.

Rule 10.05(b) The official scorer shall not credit a base hit when a:
(5) runner is called out for interference with a fielder attempting to field a batted
ball, unless in the scorer’s judgment the batter-runner would have been safe
had the interference not occurred.

Interference is not same as hit by ball:

Rule to reference is: 10.05 (a)(5)

10.05 Base Hits
A base hit is a statistic credited to a batter when such batter reaches base safely, as set forth in this Rule 10.05.
(a) The official scorer shall credit a batter with a base hit when:
(5) a fair ball that has not been touched by a fielder touches a runner or an umpire, unless a runner is called out for having been touched by an Infield Fly, in which case the official scorer shall not score a hit; o

Still learning. What about this?

Runner is out 7.08(f) (No argument here.) He is touched by a fair ball in fair territory before the ball has touched or passed an
infielder. The ball is dead and no runner may score, nor runners advance, except
runners forced to advance. EXCEPTION: If a runner is touching his base when
touched by an Infield Fly, he is not out, although the batter is out;

But what about this?
7.09 It is interference by a batter or a runner when—
(k) A fair ball touches him on fair territory before touching a fielder. If a fair ball goes
through, or by, an infielder, and touches a runner immediately back of him, or
touches the runner after having been deflected by a fielder, the umpire shall not
declare the runner out for being touched by a batted ball. In making such decision
the umpire must be convinced that the ball passed through, or by, the fielder, and
that no other infielder had the chance to make a play on the ball. If, in the judgment
of the umpire, the runner deliberately and intentionally kicks such a batted ball on
which the infielder has missed a play, then the runner shall be called out for interference.
PENALTY FOR INTERFERENCE: The runner is out and the ball is dead.

My interpretation is runner is out (interference) and batter gets FC IF the batted ball would have resulted in an out had the runner not hit the ball. If there would not have been a play, batter gets hit.

If it would have been a hit then its scored a hit if it would have been a FC then that's how it should be scored.