Story

Does the Vatican openly place a bounty for killing someone that doesn't like catholicism?

There's no such large organization for Muslims (nor for Protestants for that matter). A Pakistani politician is not comparable. There's plenty of Christian hate groups trying to kill muslims:
http://abcnews.go.com/US/man-build-ray-weapon-kill-muslims-sentenced-prison/story?id=35807538

There's much more overt anti-Muslim rhetoric from Jewish rabbis. Those "price tag attacks" against Muslims have been rather prolific.

terrorism by other factions was common in the past, but what about recently?

Everything above is quite recent. Anders Breivik's rampage was just back in 2011.

You should really have read through the links I provided and not just the HEADLINE! They do a good job answering your (loaded) questions very directly:

in 2013, there were 152 terror attacks in Europe. Only two of them were "religiously motivated," while 84 were predicated upon ethno-nationalist or separatist beliefs.
...
In December 2013, FLNC terrorists carried out simultaneous rocket attacks against police stations in two French cities. And in Greece in late 2013, the left-wing Militant Popular Revolutionary Forces shot and killed two members of the right-wing political party Golden Dawn.
http://www.thedailybeast.com/articles/2015/01/14/are-all-terrorists-muslims-it-s-not-even-close.html

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Why don't islamic countries want islamic refugees?

Turkey is taking responsibility for fully HALF of Syrian refugees, at great expense. Jordan, Lebanon, and Egypt are home to nearly all the rest. The number going to Europe is miniscule by comparison:

"In three days in September 2014, Turkey received some 130,000 refugees from Syria - more than the entire European Union had in the past three years"
http://www.foxnews.com/world/2014/11/20/amnesty-international-85-percent-syrian-refugees-in-turkey-living-outside.html

Successful Muslim (Gulf) countries like Saudi Arabia are JUST AS DISTANT from Syria as the EU is. Those same distant Muslim countries ARE now contributing significant amounts of money to support the current crop of Syrian refugees (though it certainly took them quite a while, and they could reasonably be doing more). They have some peculiar issues with taking in more refugees, which seem quite strange to someone in a western country:

"these countries are already overloaded with foreigners. For example, 88 percent of the population of the United Arab Emirates are foreigners. For Qatar, it's 85 and Kuwait 70 percent." http://www.pri.org/stories/2015-09-03/what-are-gulf-countries-doing-help-syrian-refugee-crisis

Lots more useful information is available here:

https://en.wikipedia.org/wiki/Refugees_of_the_Syrian_Civil_War