The axle is misaligned by half a stud, so an obvious approach to this problem is offset your motor by half a stud.
The technique of offsetting bricks by half a stud is known as AZMEP (from the german "aus zwei mach eins Plättchen", meaning offset of half a stud), which is a specific case of the SNIR (Studs Not In a Row) technique.
As it has been already pointed out, one way of doing AZMEP is using part 3794, Plate, Modified 1 x 2 with 1 Stud, Jumper AKA "jumper plate". You can just pop a few of these underneath your motor:
The Unnoficial LEGO Advanced Building Techniques Guide (oldie but goodie, available in gratis PDF) lists a number of other bricks that can be used for the AZMEP technique, e.g.:
I'd suggest trying out a liberal application of 1x1 round plates on the underside of the motor, clip each round plate to the space between 4 studs on the baseplate:
As Sander has pointed out, you can also use technic bushes to offset things alongside axles by half a stud. In your particular assembly, this can be useful to effectively widen the linear actuator from 3 studs to 4 studs.
I suggest the usage of 2L axle + pin plus technic bushes:
If you're short on parts, you can also consider using 2L technic pins under tension:
...but be aware that this assembly is way flimsier, and the pins will wobble around. You'll need to provide extra support to the technic 1x4 bricks (blue 1x8 in my diagram). In other words: add 6-stud wide bricks or plates to both the top and the bottom of those.
Another option is to use thin liftarms to fill that half-a-stud gap:
Finally, another solution is to forego the baseplate entirely and use an assembly attached to the motor's pin holes. Note how the motor pinholes are 3-stud wide, which are offset half a stud relative to the motor's 4-stud wide body.
There are multiple ways of achieving this, but I'll illustrate using 39793 Technic, Pin Connector Block, Liftarm 1 x 3 x 3 and 2905 Technic Liftarm Triangle:
I think the most compact solution possible needs a 92907 Technic, Axle and Pin Connector Perpendicular Split: