If you are trying to avoid having them be YOUR deck, why don't you just ask deckbuilding forums to have people build you one of each 'faction' of a deck for YOU. Now its NO one (in your playgroup's) deck!
I'm sure there are enough netrunner players that'll be more than willing to build ya a deck including the core deck and data packs.
I think his main concern is that his opponents have fun. He is experienced with card games, so making a deck would be no problem, but if his opponents aren't as experienced, this would create an advantage for him, and likely be unfun for his opponents. My roommate has played Magic for something like 14 years, I figured it would be fun to play with him, so I went and bought a starter deck. He loves building decks, so he made a deck to play against me. His deck was much stronger than mine, and by turn 3 the game was pretty much over. When I bought Android: Netrunner though, he often commented during our first few games that he "didn't know what the optimal choice was", and that he "didn't know the cards well enough to judge" his moves. This made for a more balanced, and more importantly, fun experience for me. My roommate wanted to have a list of every single card with all card effects in my deck so that he could judge his moves; I feel like that's cheating, but he thinks that over time he would learn that anyways so it would be fair. To each his own I guess.
Matias said he feels the decks are fairly balanced, thus, having other people make decks for him might create an imbalance in the deck strength, or lead to a certain deck that wins consistently; this again would be unfun for both parties. "If I use this deck I'll almost always win, and if I play against it I'll likely lose" is not much of a fun gaming situation for casual players (tournament play is a different story).
To address the original question, I guess you'll just have to wait and see unfortunately . I can't imagine that the expansions would completely imbalance the starter decks if you simply added them in, but I'm not as experienced with card games as you guys, so I'm not sure if this is a common occurrence among card games.