How did Ava get on the helicopter?

It's left somewhat vague in the screenplay. Note that it was originally a car with a chauffeur, not a helicopter:

We are too distant to hear their conversation.

But whatever is said, a few beats later, the CHAUFFEUR exits the car, and goes around to hold open the rear door, to allow AVA to enter.

Then goes back to the driver’s door.

The implication is that she simply lied to him about what was happening, then asked him to take her back to the city.

There's no indication that she killed him, nor that she flew herself anywhere.

There's no plot hole. It's explicitly laid out in the beginning of the film that the pilot isn't allowed anywhere near the place. One can easily assume he doesn't have direct contact and, as such, there's probably no reason for him to not believe who ever shows up at the designated location.

Chauffeurs often take pride in asking no questions and simply getting rider from point a to point b.

Well, there was no reason for the pilot to be alarmed. He simply flew to his boss's home when he was supposed to, in the middle of nowhere. Every order he ever received came from back home, so he'd be dazzled and easily convinced by any professional-looking person who comes from inside the very mansion he can't even get close to.

She calmly says she's the assistant, that Nathan wants to keep Caleb a few more days, and that she'll go instead... And there she goes.

https://www.slguardian.org/wp-content/uploads/2016/06/Ex-Machina.pdf

In the screenplay page 114, the way Ava communicates - which is alluded to in an earlier conversation she has with Caleb on how she can detect microexpressions - is detailed well:

The image echoes the POV views from the computer/cell-phone cameras in the opening moments of the film.

Facial recognition vectors flutter around the PILOT’S face. And when he opens his mouth to speak, we don’t hear words. We hear pulses of monotone noise. Low pitch. Speech as pure pattern recognition. This is how AVA sees us. And hears us.

It feels completely alien.

EXT. MEADOW - DAY 126

AVA and the PILOT finish talking. We are too distant to hear their conversation. But whatever is said, a few beats later, the PILOT goes the helicopter and opens the passenger door, to allow AVA to enter.

Then he goes back to the PILOT’S door. Gets in.

And the rotor blades start to turn.

I like the AI pilot theory too, but it's likely that she just manipulated the pilot into taking her away. It's a pity that this scene didn't make it into the movie.

BTW and editing re apology for zombie thread revival: I am sorry that this is awakening the dead. Just thought the screenplay would be of interest to any fan who hasn't already gotten their hands on it.

Edit: Wow. Thanks for my first badge ever - you guys rock! :)

I have a theory that the pilot is an AI as well. Oscar Isaac said that in the movie they were going to show a conversation from Ava's POV, and it was Caleb's mouth moving but nothing could be heard. You could only see waves and pulses. (Sadly, this didn't make the final cut) In the scene with Kyoko and Ava, neither communicate audibly and it's easy to assume that they've never met before and didn't know of each other; however, they fight together. It's possible that they are able to communicate a level that isn't audible or even visible, that they just manipulate these waves and pulses to interact. When Ava approaches the pilot, we don't hear communication so it's very possible that Nathan (a very secretive man who doesn't like too much human interaction) created an AI to pilot the helicopter.