To be exact, Matryona was punished in November 1724 along with her brother Willem Mons. Willem lost his head for sundry crimes -- and. most probably, for bedding Peter's wife, Catherine. I suppose Balk's story got mixed up with the 1718 Tsarevich Alexis business which saw another noblewoman knouted. Back then Peter had his ex-wife Eudoxia Lopukhina (another family member!), Alexis's mother, sentenced by an ecclesiastical court (she was a nun) to be flogged for fornication (she wasn't much of a nun) etc.
Peter died in January 1725, and Matryona didn't get to Siberia -- Catherine, not only Peter's widow but his successor on the throne, stopped Balk en route and ordered her to Moscow. The empress's mercy isn't all that surprising, given that Matryona got in trouble because of Catherine.
'... each unhappy family is unhappy in its own way.'