Laura-Pendergest-Holt denied one charge of conspiring to obstruct a Securities and Exchange Commission (SEC) investigation into SFG and another count of obstructing the investigation, the Associated Press reports.
She will now face a trial starting on July 20th. If convicted, the news agency added, Ms Pendergest-Holt faces up to five years' imprisonment on each count plus a fine of up to $250,000.
The complaint against the former CIO alleges that she failed to inform the SEC during an interview that she had met with officials representing Sir Allen in order to prepare for the meeting.
She is also accused of causing $4.3 million in Stanford bank funds to be wire transferred to the firm's operating account in Houston after providing false testimony to the SEC.
The SEC charged Sir Allen in February on suspicion of orchestrating a "massive" $8 billion deception involving the sale of certificates of deposit through the Antigua-based Stanford International Bank.
The billionaire denies any wrongdoing.