Nothing would change, there was no Samura/Hogosha alliance before the change of government and there will not be one now.
Hogosha have always done what is right by them and will continue to do so.
Before the change of government, the Hogosha would work for both Samura/Kishiro doing what ever gave them the most benefit.
Samura being the largest corp spent more money on the Hogosha to hire them for different tasks than Kishiro did, but Kishiro still used them.
Now I see Kishiro needing more of a hand from the Hogosha in certain areas and hence spending more money on them, this does not mean Samura will not continue to hire them, just that it is more equal.
Samura still represents the best situation for Hogosha as they will promise a return to the organisation prior power within Kusari.
But the Hogosha are crafty devils and will still continue to work for whom ever is willing to hand over the cash.
About Hogosha attacks on GMG, this is a non issue.
Hogosha is not able to pirate GMG ships in Kusari and as such, any piracy that happens against GMG would have to be considered GMG's problem as Kusari's hands are tied to what happens in the Sigmas unless Kusari were to annex said systems, something the GMG would not stand for.
Also Bindo, the embargo against GMG from Kusari was primarily because the GMG tried to annex a Kusari planet that was an important part of the Kusari food chain, not because the GMG attacked a couple of Samura transports.
This however is a complicated issue that can go on for quite a while, let's just say it was not for the attacks on a couple of Samura ships.