Yes! If your orthopedic surgeon hasn't told you NOT to do it...you really should follow your therapist's advice.
Studies show that exercise in the standing position after ACL repair is safe. This is true even during the early phases of rehab.
For example, during single-legged squats, the quadriceps muscle along the front of your thigh will contract at the same time as the hamstring muscles along the back of the thigh. This is called cocontraction.
With cocontraction there is very little shear force on the joint. Shear forces are normally generated when the quadriceps contract without the hamstrings. Activating the hamstrings decreases the amount of force that occurs when the quadriceps muscle contacts and pulls the tibia (lower leg bone) forward on the knee.
Your therapist will guide you through the rehab process with the right exercises at the right time. However, don't be afraid to bring up your concerns. You need to feel confident that your knee will hold you up.