I understand your considerations.
But, well, as I said before, it is much more easier for a Pirate to take control of a PC than a Switch, a router, or an IP Phone.
Since as I said before I' m using VLAN.
A pirate compromising a PC on a Data VLAN would have no chance to get on the Voice VLAN where Telco equipements are trusted and less exposed to piracy (IE, applications, e-mail, etc...).
Of course, you could have VLAN separated trafics and use DSCP QOS.
But with L3 QoS and DSCP (or IP precedence) you have a weak point at the connection between the Fortigate and the Switch where you would have to re-mark DSCP fields coming from untrusty PC in order to prevente abuse.
On L2 QoS, the packets coming from PC are untrusted. Whatever comes from them is set with lower CoS (802.1p). This is automaticaly and efficiently performed by L2 equipements (switches). Processing remains at level 2.
With L3 QoS you have to build Policies in order to remarks paquet' s DSCP field either for each ingress port, or for the egress port going to the firewall.
More over, L3 QoS require more processing and therfore expencive devices with stronger process units and smarter processing, and finally use more power which is neither good for the planet nor for the accounting of the enterprise.
The IT team as well spare time and ressources for implemeting easier CoS L2 instead of more difficult L3 QoS.
One rule in engineering : KISS (Keep it stupidly simple).