If there is a silver lining behind the failure last month of Penn Square National Bank, it's that big depositors likely will be more careful about where they put their money, Federal Deposit Insurance Corp. Chairman William Isaac says.

Exposed customers--mostly credit unions and savings and loan associations--could lose as much as $50 million of the $250 million in uninsured deposits at the Oklahoma City bank. Isaac's agency guarantees accounts up to $100,000.

The discipline that the sophisticated investors place on the banks they lend their money to (a deposit is, in effect, a loan) are an important check on the banking system, both Isaac and Comptroller of the Currency C. T. Conover told Congress. Conover closed Penn Square. Isaac's agency took over as receiver.

But credit union officials, supposedly the sophisticated investors who could have put a check on Penn Square's lending spree that led to its ultimate demise, say there is no way they could have known the bank was in trouble.

Peat, Marwick, Mitchell & Co., the bank's new auditors, gave Penn Square a virtually clean bill of health for 1981 in a public report issued March 19, 1982.

The bank's profitability was strong and it seemed to have adequate capital. Officials of several credit unions said they had the bank's "numbers" analyzed by reputable consulting firms and felt confident that Penn Square was reasonably strong.

What investors did not know was that Penn Square had been under "special supervisory attention" by the comptroller's office since early 1980 and that Peat, Marwick had done a second analysis--for management and directors only--that highlighted weaknesses in the bank's policies and procedures.

But financial experts said that the big investors should have spotted red flags anyway. Penn Square fired its 1980 auditor, Arthur Young & Co., after the accounting firm gave the bank a "qualified" report. Furthermore, the bank often was paying far more for deposits than other comparably sized banks.

James Blanton, managing partner of the Peat, Marwick office in Oklahoma City, said a financial statement by itself does not tell potential investors enough about the health of a company. Blanton said Peat, Marwick still stands by its 1981 audit, but cautioned that it is nothing more than a snapshot of the bank's position on Dec. 31, 1981.

"We talked to Penn Square officials who assured us the bank was fine," said one credit union manager. He admitted he was a little leery because the bank was offering large premiums on deposits, but said he was told by Penn Square officials that it was because the bank needed the money for a month to finance a "big, solid loan."

The credit union put more than $1 million into a one-month deposit at Penn Square, only $100,000 of it insured by the Federal Deposit Insurance Corp.

Yet, the credit union manager conceded, when the month expired the deposit was renewed at another premium interest rate, even though Penn Square's urgent need for the money presumably had ended. "It just wasn't as big a thing to renew," the manager said.

Furthermore, said one federal regulator, anyone who read the Peat, Marwick report would have discovered on the first page that the previous year, Arthur Young & Co. issued a "qualified" report on Penn Square because the bank's paper-processing procedures were such a mess that the accounting firm could not satisfy itself that Penn Square loans were adequately collateralized.

"Anytime you find an auditor fired after he gives a qualified statement, it's time to be wary," said an official of a major accounting firm who asked not to be named.

Peat, Marwick, after noting the Arthur Young reservations, said that the bank had "formalized its approach to" documenting loans and that it felt Penn Square's financial statements "fairly" represented the bank's position.

Conover, in an interview, agreed that nothing in the public financial statements required of Penn Square by themselves painted the picture of a bank with a troubled loan portfolio. Furthermore, he said, the increased disclosure bank regulators would like to require probably would not have triggered any further warning signs.

The steps the comptroller took to try to bring Penn Square back into line will be the subject of public debate for some time. Bank officials essentially ignored first pressure, then an agreement with the comptroller's office to change their ways. Many congressmen--as well as officials of some of the credit unions that were burned--believe the comptroller should have removed Penn Square's management.

Conover said that until the audit begun last April--the audit that uncovered so many bad loans that the bank was closed within three months--there was no evidence of the kind of wrongdoing that would have justified removing management.

The big depositors and the big banks like Continental Illinois and Chase Manhattan that bought bad loans from Penn Square were guilty of bad judgment, according to Lawrence Fuller, banking analyst for the brokerage firm of Drexel Burnham Lambert Inc. Analyzing numbers is not enough, he said.

Another analyst said that in the last few years, too many investors--banks as well as individuals--have been so concerned about getting the highest return for their money that they have ignored credit risk. "What good does it do you to get 16 percent on your money," he asked rhetorically, "if you lose it?"

About 150 credit unions and 20 savings and loan associations with uninsured deposits in Penn Square presumably know the answer to that question.