As PFT (Profootballtalk.com) correctly articulated [last] week, prior to participating in rookie minicamps, drafted rookies "without contracts" sign Injury Protection Letters which basically say that in the event that the player suffers a season-ending injury, the club will still negotiate a contract in good faith as if the player weren't injured.
I say "without contracts" because if you were to look at your favorite team's salary cap today, you'd see that your draft picks are actually counting against your team's cap, meaning they are indeed contractually bound to the team right now. You may ask how are they contractually bound to the team without a contract? It's called a rookie tender. When a player is drafted, the club technically tenders the player a 1-year contract for the salary minimum of a player with 0 minimum salary credits (in 2009, this amount is $310,000). So all draft picks with the exception of Matt Stafford, have P5 salary amounts of $310,000 right now; until they negotiate their real contract. Without these rookie tenders, the player would not be contractually attached to the team.
Back to [the Patriots's] McKenzie and [the Saints'] Arnoux, their circumstances aren't unique, FS Sean Jones, who signed a UFA contract with Philly this off-season, as a 2004 2nd Round pick of the Browns tore his ACL in minicamp. Similarly, WR Drew Carter as a draft pick of the Carolina Panthers also tore up a knee prior to negotiating his rookie contract. So it's not a unique occurrence, and the precedents set by these examples and others show that team's do indeed negotiate in good faith and that there aren't any differences in their contracts because they're injured at the time of the negotiation.
In 2008, the Eagles drafted in the 4th round DB Jack Ikegwuonu, who prior to the draft blew out his knee while preparing for the combine. If you look at Ikegwuonu's contract compared to the Eagles' other two 4th round draft picks in 2008, you'd see that his contract is structured the exact same and doesn't standout in any way as result of the player's injury.
I'm sure McKenzie and Arnoux are disappointed about their injuries, but from a contractual standpoint, they can rest assured that their injuries will not impact their deals.
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J.I. Halsell has 4 seasons worth of NFL Salary Cap and Player Contract experience. For 2 seasons, he was the Salary Cap Analyst for the Washington Redskins, where he played a role in every player contract negotiation to occur during that period. Prior to his stint with the Redskins, he worked for 2 years for the NFL's labor relations department, the Management Council. You can read more of his writing on his blog INSIDE THE CAP with J.I. Halsell