The Minbari didn't believe that Sinclair was "related" in any genetic sense to the Minbari. They believed that a Minbari soul had been reincarnated in him. There's a difference. (Because the Minbari believe that souls are reincarnated in the next generation, and because the Minbari population has been in decline for 2,000 years, and perhaps sharp decline for 1,000, there are "missing" souls that must somehow be accounted for. The glowing triluminaries - because they also scan other pilots at the Battle of the Line - suggest to them that these souls are being reborn into Human bodies.)
The Council thus accepts that the war must end because "Minbari must not kill Minbari", but they are by no means unanimous in their beliefs regarding Sinclair and his relation to the Minbari. Some believe he is Valen returned, others believe that he has
some Minbair soul, perhaps even a Great Soul, but not Valen's, some don't believe any of it. This spilt explains their rather schizoid approach to Sinclair. They have him appointed commander of B5 because that somehow seems to accord with prophecy, but they order Delenn to watch over him and to kill him if necessary. (Delenn doesn't
refuse the order to do so. It is more accurate to say that the precise conditions that would trigger it - his regaining his complete memory of what happened at the Line and her
being aware that he has - never come about.)
They think he had a Minbari soul, perhaps even Valen's. They never for one second imagine that he might
be Valen. Valen deliberately leaves them just enough information for them to do what they must do in the 2250s and 60s, without endagering the timeline. Delenn knew nothing of Valen's true identity until she received the letter.
As for Delenn knowing/suspecting where Valen came from (this would limit the possibilities of who could become Valen)... she had seen pictures of Babylon 4 in Minbari use, and surely recognized the design on arrival to Babylon 5.
That would suggest it was a Human.
I don't think Delenn had any reason for suspecting that anyone would "become Valen". I think we're projecting our own knowledge onto the characters. Delenn
did recognize the design of the B5 station as similar to that of the Valen's station when she arrives to open her embassy, and she verified her suspicions by checking photographs of B4 itself. This certainly left her with a mystery, but no basis for making
any assumptions about who was responsible for its apparent trip through time. The Humans, in fact, might have been near the bottom of her list.
1) Despite B4's being a Human station, with a Human work crew bringing it on-line at the time it disappeared, it apparently arrives in the 13th century with only two beings aboard it - a Minbari named Valen, and an alien of unknown origin called Zathras. There's no sign of the original crew. That the station later materializes and has the crew evacuated in 2258 leaving only the alien Zathras and the ghostly space-suited figure aboard only deepens the mystery.
2) Delenn says that the Minbari have no way to control a time field "this unstable". That suggests that the Minbari have
some technology that involves time, and some ability to manipulate it. That makes the Minbari themselves far and away the most likely race to have engineered the theft of B4.
3) The matter of Valen being "a Minbari not born of Minbari" does not necessarily suggest that Valen started life as some other species and then changed. We only see it that way because we know the whole story. The phrase itself no doubt originated because one he returned to Minbar, Valen had no satisfactory way to account for himself. In a society ruled so strongly by family, clan and caste, it would have been immediately obvious that
Valen had no realtives, no history, no employment or school records... Imagine someone running for President or Prime Minister today who could not produce a driver's license, a family, a school transcript or a birth certificate. The adult "orphan" Valen had to be explained. But that would have been as true if he'd been a clone created in a Vorlon lab or a time-travelling Minbari as in any other case. And saying that he was a "Minbari not born of [any living, known] Minbari" would have been as true of the clone or the time traveller as of Sinclair.
4) OTOH, B4 vanished years before either the Minbari or Sinclair became associated with the Babylon Project - which suggests that some other agency was responsbile.
Regards,
Joe