Electrical – Any cheap and easy ways to isolate analog signals

You need to add flyback diodes and base resistors to your circuit, and you need something more substantial than a 2N2222 as a driver.

Also, if the opamps driving the bases can't source enough current to drive the transistors into saturation, you might want to consider using N MOSFETS instead of bipolars for the motor drivers.

Finally, if you're getting interaction between the two sides, it wouldn't hurt to stiffen up your 5V supply and make sure all your grounds are solid, or use a separate supply for the motors, still making sure all the grounds are adequately sized and solidly connected.

Basically, from an electrical viewpoint, every "digital" signal is as you say, only an approximation of a square wave. In particular it will have finite rise and fall times.

At high speeds, it can be difficult to ensure it looks as nice as the theory wants. To ensure that the signal is still detected as digital (i.e. the receiver doesn't get utterly confused by a horribly shaped signal), the so-called eye diagram (aka eye pattern) is used to measure its characteristics over a number of samples.

Many standards (e.g. USB and what not) define some acceptable characteristics for this diagram.

Note that an eye pattern/diagram isn't restricted to just two [voltage] levels. It's also applicable when you have any number of discrete output levels. For example, Gigabit Ethernet over twisted pairs (1000BASE-T) uses not two but 5 different voltage levels.

Is it just our interpretation to whenever the voltage passes some barrier or falls under it? Meaning, when the voltage is above some arbitrarily chosen threshold we consider it as "high" but otherwise we consider it "low"?

Basically, yes, that's how it works, some voltage thresholds for what is "1" and what is "0" are decided by a some standard.