It is not as much anti-religious as anti-establishment.
V can be seen as an anti-protestant vigilante because the government is using the Church of England as one of its method of control of the population. It doesn't mean it is pro-Catholic or pro-Muslim, even if we see that possession of Quran is a punishable offence: Islam is banned because of the St Mary's attack were blamed on Muslim terrorists and the Party has rallied people under the banner of xenophobia.
Now please note that it is never mentioned that the Guy Fawkes was a Catholic fighting Protestants - he is displayed as someone willing to fight with the system because he thought that the persecution of people based on their beliefs is wrong. Which is more or less historically accurate: the Gunpowder Plot was trying to kill the unjust (in their opinion) king, not protestants; they were planning to blow up the parliament, not the Westminster Chappel
The plan was to blow up the House of Lords during the State Opening of Parliament on 5 November 1605,[a] as the prelude to a popular revolt in the Midlands during which James's nine-year-old daughter, Elizabeth, was to be installed as the Catholic head of state. Catesby may have embarked on the scheme after hopes of securing greater religious tolerance under King James had faded, leaving many English Catholics disappointed.
On 19 February 1604, shortly after he discovered that his wife, Queen Anne, had been sent a rosary from the pope via one of James's spies,[d] Sir Anthony Standen, James denounced the Catholic Church. Three days later, he ordered all Jesuits and all other Catholic priests to leave the country, and reimposed the collection of fines for recusancy.
Wikipedia: Gunpowder Plot
The movie portraits Guy Fawkes (and V) as a hero fighting the corrupted system, not someone fighting for/against certain religion, someone who is standing in defence of people persecuted for daring to be different than the system would like.
While the Church of England in the movie might be displayed as a corrupt institution, I don't believe that was the purpose of the movie - its the country that is sick, the Party that used its influence to promote a paedophile priest to the position of bishop.
Now regarding the last few points:
the people that V kills are presented as either stereotypically protestant or at least stereotypically Anglican (as far as I know there is little difference)
For me, those people are stereotypically BRITISH. Neither of them (including the bishop) is displayed as a religious figure and by looking at them I couldn't say (but then I am not British myself) are they protestant, catholic or cultists of Cthulhu: they drink tea, and say "bollocks" a lot. When God and religion is ever mentioned, it is always in the context of Party:
So I read that the former United States
is so desperate for medical supplies...
... that they have allegedly sent several
containers filled with wheat and tobacco.
A gesture, they said, of goodwill.
You wanna know what I think?
Well, you're listening to my show,
so I will assume you do.
It's high time we let the colonies know
what we really think of them.
I think it's payback time for a little tea party
they threw for us a few hundred years ago.
I say we go down to those docks tonight
and dump that crap...
... where everything from
the Ulcered Sphincter of Ass-erica belongs!
Who's with me? Who's bloody with me?!
Did you like that?
U.S.A., Ulcered Sphincter of Ass-erica.
I mean, what else can you say?
Here was a country that had everything,
... and now, 20 years later, is what?
The world's biggest leper colony. Why?
Let me say that again.
Do I have to mention that the USA is a predominately protestant country? The religion is used only as a tool, a method to justify the Party's work:
... homosexuals, terrorists.
They had to go.
Strength through unity.
Unity through faith.
I am a God-fearing Englishman,
and I'm goddamn proud of it!