Whether it is legal to give half point byes in a FIDE Rated Swiss tournament has been subject to debate for quite a while. Some pairing programs do allow it (even FIDE approved ones) but until recently the pairing rules seemed to be clear that it wasn't allowed. Under the rules for the Dutch System clause F5 stated
However the last meeting of the FIDE Swiss Pairing Programs Committee, as well as the FIDE Technical Commission had a look at the rules and have now ruled that they are allowable.
In the updated Swiss Pairing Rules clause B1b now states
The text of the updates Swiss Pairing Rules is at this link FIDE Swiss Pairing Rules (Dutch System)
(Note: Clause F5 still remains unchanged in the updated rules, but in discussion with SPP Chairman Christian Krause, we agreed that this is overridden by B1b and F5 will be changed at the next meeting).
The discussions concerning this, and other changes to the pairing rules are included in the minutes of the Swiss Pairing Programs Committee.
However the final decision of half point byes was made by the Technical Commission, who's meeting minutes are here.
Nonetheless there may be some time until all FIDE approved pairing programs are updated to reflect the changes in the pairing rules. At the 2012 Queenstown International I observed a number of cases where players who had received a half point bye were then downfloated in the next round, or the round after by Swiss Manager. on the other hand, JaVaFo, which we ran alongside Swiss Manager (under the Vega interface) did treat the half point bye correctly.