Means to an end, justified or not?

The end justifies the means. What is your opinion?
Consequentialism states that a morally right action is one that
produces a good outcome. This can, however be disputed as it can also
hold the meaning for a corrupt act leading to good ‘consequences’
which is either almost not possible or achieved through means of
deception.
I cite the example of Galileo Galilei who questioned the Copernican
system in 1624 by debunking the teachings of the Christian doctrine
which held that the sin was the centre of the universe. He was
eventually convicted and sentenced to house arrest in Florence, Italy
where he died in 1642. If we were to take the direct results of his
actions against the Christian doctrine, which is house arrest,
ridicule and death we will be forced to conclude that his act was a
morally wrong one which befits his demise. However, we know now that
he was a great pioneer of scientific teachings and was the first to
discover that correct universal law and despite his demise we
appreciate how great a scientist he was.
Another example of a battle between Spaniards and the Incas would best
support my opinion on how often times the ends do not justify the
means.  The battle of Cajamarca on November 16, 1532 as written in the
book Guns, Germs and Steel by Jared Diamond was between the Inca
Emperor Atahuallpa and the Spanish Conquistador Francisco Pizarro. The
former led a ragtag team of one hundred and sixty eight Spanish
soldiers in unfamiliar territory towards where Atahuallpa was
protected by eighty thousand. Despite this vast difference in manpower
Pizarro managed to capture the King and hold him in hostage until he
extracted a large ransom and reneged on his promise to free the king
by executing him.
Pizarro took advantage of the lack of knowledge and experience the
Incas possessed of Spaniard military prowess (steel swords, guns and
steel armor) by using the artillery against them. The Incas who has
never before head the blaring of trumpets and the cracking of guns
were thrown into disarray. Atahuallpas troops had only stones or
wooden clubs, which would at best only injure the Spaniards and wore
quilted armor which offered them no protection from the bullets or
steel swords.
Consequentially, since the Spaniards won the battle, we’d have to
accept that their method of fighting, which was by tricking the Incas,
using their own weakness against them and breaking their word when the
Incas were at their weakest, was morally correct. The massacre of
eighty thousand soldiers would be nodded away without another thought
and their sacrifice to protect their homeland against intruders be
waved away as a mere stupidity.
The essential judge cannot be consequence or outcome. It is wrong to
simply judge an act by its consequence because the reason behind that
act, its intention is just as important in decided what makes it
ethically correct.