[merylsilverburg]

The reason why the ending ended the way it did is because the mangaka (Kouta Hirano) wasn't finished with the manga. There's only 4 volumes of Hellsing out and there's supposed to be more. So, that's why the ending was arupt and confusing.
I'm no expert on this series but this is what I think: (I've been trying to figure it all out ever since I saw the end in May )

Integral didn't betray the Hellsing organization. What happened is Incognito started to send out his vampire troops (SAS) to go and destroy the Royal family. Those two men dressed in black (short and tall guys) went to Integral to tell her that this ritual (I have no idea what it does) is supposed to be held. The news said the ritual is being held at the Tower of London and the Queen is going to be there. So, Incognito sends his SAS vampires there to wait for the Queen. Instead, the Tower of London was just a bait and the ritual is really held at the Hellsing mansion. In order to get rid of these SAS vampires, Integral sends out the Hellsing unit to go to the Tower of London. But, the Tower of London really was a trap for the Hellsing unit. I think that's when Seras was at Helena's and she found out. At the Tower, the Hellsing unit are getting killed by the SAS vampires and then, the British army arrives with an order to kill the Hellsing unit (I don't know why...I think there was a traitor in the Round Table group. The Round Table is that group of snooty men during the Valentine Brothers episodes). The British troops are also invading Hellsing's mansion and that's when Integral and Walter escape in the helicopter.
And the rest follows. I think the reason why Integral was jailed is because they thought she was a traitor who wanted to kill the Queen or something like that. Either that or that Round Table group wanted to get rid of her. Either way, the Queen didn't show up at the Hellsing mansion like the plan said, so someone's a traitor, but I don't know who.

Ahh...I hope this helps...a little.