from a RP point of view: no, its not OK ( in general )
edit: let me elaborate that....
RP wise, bretnoia is at war - and its not like they re on the winning side much. - they are short on resources, ships, personell. - a freelancer is a factor of uncertainty ( hence he is a freelancer ) - giving him a gunboat means not giving a BAF a gunboat command. - now the BAF is a reliable factor. - so that BAF would rather choose the reliable factor over the uncertain one.
from a point of view whats logical and possible - sure...
what you should do it to cooperate with the BAF| playerfaction about it - discuss it with them, give them a heads up what you want to do.
and most importantly - while plying ingame - reflect your good relationship to the BAF
so, its not only fancy story writing, but its actually RPing ingame that you are an independent freelancer that is allowed to fly military hardware from a house that is currently at war with another house. - so i daresay, you might not be "freelancing" at all when you get your ship... ( but you might still be a freelancer by ID )