Runner on base out when hit?

[emaxos]

I ususally stay in the softball board but I was told about a situation that happened in Dixie baseball that I wondered about.
R1 on first, defense playing behind the bag. Batter hits a soft popup toward first base, in front of the defense. R1 steps off 1st with one foot, then brings foot back to the base. R1 is has both feet on the base and the ball hits his leg and caroms toward second base as the defender is coming in. BU calls R1 out because he was hit by the ball.
Seems to me that vacating the base to avoid interference would put him in jeopardy of being tagged out or doubled up if catch was made. Isn't the base considered a safe haven?