It could just be Big Boss stuck between a rock and a hard place where because of The Patriots, he has to send Solid Snake in to fight Venom... he feeds him wrong info to keep Venom alive as long as possible, but has faith in Solid to survive all the shit he puts him through, cause at the end of the day... both are his "sons"?
I dunno, I'm spit-balling here.
From the truth tapes, real BB doesn't seem to have any familial bond to his "sons" at all. He said he will just treat them like a normal person. He sent SS on the mission in hopes that he failed, and didn't expect him to succeed in killing Venom. SS successfully kill real BB in MG 2. Well, this is all my conjectures.
My only issue is who the heck was in charge of Cipher/Patriot during this time period, since Zero should be incapacitated after suffering that parasite attack. I don't find Dr. Clark and Donald Anderson to be capable leader/mastermind. The AI/Patriot still have to operate within a certain parameter set by Zero so they shouldn't be that formidable. Why would real BB with Batman Ocelot at his side be afraid of a cripple Cipher? I hope there is part 6 to answer some of these questions.