Squats can be done safely with an injured ACL.
In Effects of technique variations on knee biomechanics during the squat and leg press (also available here for free), the authors found that "no ACL forces were produced for any exercise variation" of the squat or leg press, and that "the lack of ACL forces implies that all exercises [squats and leg presses] may be effective during ACL rehabilitation".
In Knee biomechanics of the dynamic squat exercise, the authors conclude:
The squat was shown to be an effective exercise to employ during
cruciate ligament or patellofemoral rehabilitation. For athletes with
healthy knees, performing the parallel squat is recommended over the
deep squat, because injury potential to the menisci and cruciate and
collateral ligaments may increase with the deep squat. The squat does
not compromise knee stability, and can enhance stability if performed
(By parallel, this means tops of the thighs parallel to the ground.)
The deadlift also.
From A three-dimensional biomechanical analysis of sumo and conventional style deadlifts:
Because the deadlift is considered a closed kinetic chain exercise
(23), it can also be employed in knee rehabilitation programs, such as
after anterior cruciate ligament (ACL) reconstruction. Numerous
studies have already shown that the squat is an effective exercise
during ACL rehabilitation (11,15,20,22,25,26,29). Because the deadlift
is performed in a similar manner as the squat, it is hypothesized that
the deadlift may provide similar benefits during ACL rehabilitation.
The moderate to high hamstring activity that has been reported during
the deadlift (28) may help protect the ACL during knee rehabilitation.
However, which deadlift style would be most effective in knee
rehabilitation has not yet been established.
Leg extensions are not recommended for an injured or recently reconstructed ACL.
(You didn't ask about leg extensions, but jp2code suggested them, so I'm correcting that here.)
Many studies (for example, Electromyographic Evaluation of Closed and Open Kinetic Chain Knee Rehabilitation Exercises) have shown that open kinetic chain exercises (leg extensions) produce significantly higher shear force at the knee joint. These shear forces result from increased quad tension and can direct too much force through an injured or reconstructed ACL. The authors cite 10 other authors that warn against open kinetic chain exercises after ACL reconstruction. "Because [...] shear forces are are increased during leg extensions, it seems prudent to select alternate exercises to strengthen the quadriceps after ACL reconstruction."
Regarding closed kinetic chain exercises (that includes squats), they say "weight bearing, closed kinetic chain exercises cause less elongation of the ACL than non-weight bearing, open kinetic chain exercises", and "closed kinetic chain exercises have been found beneficial in ACL rehabilitation programs".
One doctor's ACL rehabilitation program goes so far as to say "the leg extension machine should never be used because it will significantly aggravate your PF pain and can cause severe ligament injury" (emphasis theirs).
Later on in recovery, inclusion of leg extensions can assist in regaining quadricep strength and an earlier return to sport (from Closed kinetic chain alone compared to combined open and closed kinetic chain exercises for quadriceps strengthening after anterior cruciate ligament reconstruction with respect to return to sports: a prospective matched follow-up study), but the authors of that study agree that unrestricted open kinetic chain exercises could put too much strain on the ACL and suggest a wait until 6 weeks and only include them under controlled conditions.
Here's a less scholarly reference that gives a good summary of the forces on the ACL during squatting and leg extensions: