Then you just put a clause in the contract saying..(words to the effect) that this is not a bribe, and IBM does not expect any special treatment in any future dealings.
It would be nice if it were that simple... however, look at it as such:
The Pentagon has been evaluating IBM's system for purchase. This implies that it is likely that they were also evaluating similar systems from other companies. Let's say XYZ Corp. has a similar system in evaluation as well.
Now comes IBM's offer of giving the government some number of computers/licenses for free. Regardless of the rationale behind the offer, if you're XYZ Corp., you're going to see this as IBM getting an unfair advantage toward a potential larger/longer-term contract.
Many of the procurement and gift rules the government works under seem asinine, but there's a reason for most of them.