I believe it would be possible because the Harvesters already showed that their technology was compatibles with ours.
Before the first wave of the attack David discovered that the Harvesters were using our satellites to communicate with the mother ship by embedding their own signal. Dave already worked out that the signal was recycling itself into nothing
David: I've got a lock on the signalpattern. We can filter it out.
Marty: Huh? Oh, good, hood.
David: Strange thing is, if my calculations are right it'll be gone in approximately seven hours anyway. The signal reduces itself every time it recycles. Eventually it will disappear. Are you listening?
The plan was to use this same signal.
David: I gave it a virus. A computer virus.
General Grey: Are you telling us you can send out a signal that will disable all their shields?
David: Just as they used our satellites against us, we can use their own signal against them.
David: If we plant the virus directly into the mother ship, it would then filter down into all the corresponding ships below.
Nimziki: And just how do we infect the "Mother Ship" with a virus?
David: We'll have to fly their craft out of our atmosphere and dock with the mother ship. We can enter here, upload the virus and set off an explosion that could disable it. This would disorient the smaller ship below and buy you some time to take them out.
Nimziki: This is ridiculous.
General Grey: How long would their shields be down?
David: Once they discover the virus it could be a matter of minutes.
So what do we know
- The Harvesters technology is compatible enough that they could use out Satellites.
- The Harvesters signal interfered with our own, evident by the distorted TV signals everyone was getting.
- The Signal could be separated with our technology, as per David's suggestion before he realized what it really was.
David also had the previous research done by Area 51 who had one of the Harvesters' ships which crashed in Roswell about 50 years prior. When his Father gave him the idea for the Virus he wakes up one of the Area 51 Scientists. While it had been largely inactive they did repair it since and it did come alive recently and the time since the Harvesters first appeared they probably worked out if at the very least it's systems ran off a Binary System like our computers.
The fact that the ship alive when the Harvesters arrived was an indicator that the ship could probably still intact with the Harvesters other ships (one could assume that it came alive when the signal was first implanted). If you could infect that ship you could at the very least transmit the Virus from that Ship into the Mothership when the 2 connected since apart of the plan was to would disorient the smaller ships with the Mothership's destruction. To alter David's Joke about giving the Area 51 Ship a Cold, the Area 51 Ship could be used like a Patient Zero.
Don't forget how smart David is. Not only did he discover and learn the nature of the signal he got Constance's number, used her in use phone to triangulate her position inside the Whitehouse and guided her to a nearby window which he and his father could be seen from. He also anticipated the Virus being counteracted within a matter of minutes and volunteered for the mission thinking of what he might need to do if anything went wrong rather than making a 1-click install package for someone else
Constance's: With you? I don't understand why you can't just show someone how to plant the virus, somebody trained for this kind of mission?
David: If anything goes wrong I'll have to think quickly, adjust the signal, who knows?
I suspect that the Virus was a rush job so don't expect a well documented, well formatted piece of programming art
Script Sourced from Internet Movie Script Database