This article is from the The Terminator FAQ, by Karsten A. Loepelmann firstname.lastname@example.org with numerous contributions by others.
The T-1000 could have taken either shape; since the T-1000 took the shape of
the guard at Pescadero, it would seem that the T-1000 could have taken the
Terminator's shape as well, or at least come close to resembling him. It may
have thought it would have had a better chance of getting close to John if it
took the shape of his mother. Don't forget that the T-1000 had no information
on how John's relationship was progressing with the Terminator, so it would
assume that Sarah would have been a better choice.
The Special Edition indicates that this behaviour resulted from the damage
experienced by the T-1000 after being frozen and shattered.