The state of Virginia yesterday said E. F. Hutton & Co. has paid $50,000 as part of a "settlement and compromise" of the state's followup investigation of Hutton's guilty plea to 2,000 federal counts of mail and wire fraud for a check-kiting scheme.

The order does not explain the payment, but the money is believed to be reimbursement for investigative costs incurred by the State Corporation Commission.

The state order confirmed that Hutton had reached a severance agreement with Perry H. Bacon, who was manager of the firm's Alexandria branch in November 1981 when it was overdrawing its United Virginia Bank checking account by an average of $9 million a day.

Hutton attorney Terrence B. Adamson said the terms of the agreement, which permitted Bacon to resign, are confidential.

The order cited a September report in which former U.S. attorney general Griffin B. Bell said that Bacon was "responsible for enacting and supervising" the scheme and quoted Bacon's admission that the branch wrote checks not only on "deposits plus anticipated deposits, but also bogus deposits."

The order, which removes the possibility of a proceeding to revoke Hutton's securities license on the ground that it has been convicted of a felony, includes these additional provisions:

*Hutton will use local checks for payments to those Virginia customers who specifically request this.

[The commission said no customer funds were involved in the abuses that led Hutton to plead guilty and pay a $2 million fine.]

*Hutton is disqualified from using Virginia's simple, speedy "short form" registration for securities offerings, but can seek a waiver of the disqualification after next April 15.

*Hutton will make quarterly reports on its compliance with the Virginia Securities Act.

Adamson said there has been "no resolution" of investigations either in the District, where Bacon managed a branch after leaving Alexandria, or in Maryland.

In addition to Virginia, Adamson said, the only other states that have signed consent orders with Hutton are Georgia and New York. Ohio has agreed to an order, but has not made it official.

In Connecticut -- the only state to hold public hearings -- Attorney General Joseph L. Lieberman has urged the Banking Department to suspend Hutton's license for 30 days and fine it $500,000.

The company has labeled the proposed punishment "absurd," partly because it would hurt innocent customers and employes of a company that has become what it says is "the most thoroughly rehabilitated corporation in American history."

A far-reaching Securities and Exchange Commission consent order on Oct. 29 barred Hutton from opening any new retail brokerage offices for 120 days and required the firm to pay more than $1 million to shareholders of Hutton-managed investment companies who were improperly deprived of earned interests.

The SEC also ordered a series of new internal controls to prevent future cash-management abuses, pledged hearings on whether Hutton should be disqualified as an investment adviser, severely criticized laxity in senior managers, and promised to continue to investigate "to determine whether enforcement actions against individuals or other entities are appropriate."