Thomas, 29, is currently involved in a custody dispute with her former husband, Sandusky's son Matt.
Judge John M. Cleland, who issued the pretrial order involving the other children, opted to leave any decisions involving Thomas' brood to the judge presiding over her custody case.
"I cannot understand how a court could place the desires of someone who is criminally charged with sexually abusing children above the safety of children," Thomas said. "I will continue my fight to protect them in hopes that at some point, someone in a position of authority will do what is necessary."
An attorney appointed to represent the interests of Thomas' children in the custody case has recommended they be allowed to visit Sandusky but under strict restrictions.
Sandusky's attorney Joseph Amendola insisted that Thomas was only trying to use the criminal charges against his client to bolster her own custody claim.
"Unfortunately, Jerry appears to have been dragged into this battle," he said. "We have the utmost faith that the judge will make his decision based upon the best interests of Jerry's grandchildren."
Sandusky has denied charges that he molested at least 10 boys he met through The Second Mile, a charity for disadvantaged youth he founded in the '70s.
But soon after his November arrest, Thomas told authorities that the former assistant coach had "inappropriately touched" her son.
Earlier this year, the Centre County Children and Youth Services office found those allegations to be unfounded, Amendola said.
State child services workers typically do not discuss their investigations publicly.
But on Monday, Thomas characterized their findings as simply a determination that there was not enough evidence to charge Sandusky for the abuse.
Sandusky is set to take his criminal case before a jury in May.
Contact staff writer Jeremy Roebuck at 267-564-5218, email@example.com, or @jeremyrroebuck on Twitter.