A Virginia judge yesterday struck down a probation agreement that had banished Thomas E. Bruce, a 28-year-old mentally ill Vietanam veteran, from his home near Charlottesville.

But the judge's order still prohibits Bruce, who now lives in a Northwest Washington apartment, from returning to his rural hometown of Esmont without the approval of his probation officer.

Bruce's banishment, ordered under an agreement worked out by an Albemarle County prosecutor and Bruce's defense layer, has been labeled "unconstitutional and unenforceable by state Attorney General J. Marshal Coleman.

Bruce was convicted of shooting a store owner in Esmont on Feb. 23, 1978. He subsequently was charged with murdering an Esmont man December 4, 1978, while out on probation for the earlier offense.

The murder charge was dropped, but emotions in the southwest Virginia community continue to run high, and there is fear that if Bruce returns an attempt may be made on his life, Albemarle County authorities say.

Under the amended probation order issued yesterday in Albemarle County Circuit Court, Bruce is to be supervised by District of Columbia authorities and is to continue to undergo psychiatric treatment, according to Tom Wilson, an Albemarle County probation officer.