When is it justified to use terror tactics to achieve a goal? When does it become the obvious next step to take hostages or plant bombs? Is it possible to threaten civilians and still remain justified?
It would take having genuine cause to believe that it is a "them or us" situation, I think. One dire enough to make becoming a murderer or worse appear preferable to the alternative.
Is it possible? Perhaps if they are shooting back and there is no hope of convincing them otherwise. Big if.
Otherwise, only in sci-fi scenarios akin to a zombie apocalypse.
If you religion is being oppressed? If someone is mocking everything you hold sacred? Is it when you can see no other way to get your government to change it's stances on an issue that is of vital importance to you?
In and of themselves, those are, at the very least, odd things to complain about.
Religion is a private affair. Other people have no particular duty to lend it prestige. If it bothers me that they do not, them that is my problem, not theirs.
It is entirely possible for governments to be oppresive and that must be fought against. But the lines drawn have no reason to acknowledge any religious beliefs or doctrines.
In fact, they should actively avoid making such acknowledgements, lest they end up lending some religious doctrine the power to oppress those who do not share of it.
The other side of that coin might be when is it okay to take away the rights of your citizens? Can you ever reasonably justify taking away part of the right of privacy or free speech? Should we stop places like Saudi mosques from being opened in the western / eastern world?
Ultimately, despite a lot of willingness to claim otherwise, there are no citizen rights that might conceivably be taken of by someone. There is even a logical contradiction in the very idea.
People do not have "rights". Instead, we have the gifts that are given to us by ourselves and others.
Whether mosques (or any other temples) should be opened is entirely a matter of how much public acceptance those projects expect to have in their respective communities. Barring legitimate public concerns, it is not for any government to interfere, either pro or con.
Is there ever a time when it is okay to don the jackboot in the name of safety? Should you stop places like the westboro Baptist church from protesting at funerals or is that not far enough to warrant government intervention? When would the acts of a religious organization or their teachings warrant intervention?
When they violate civil peace and urban order. Westboro probably qualifies. So does KKK. So, apparently, do most Muslim-majority communities, mainly because they tend to expect undue privileges and assurances that end up translating into repression of non-Muslims.
Does it just fuel the fire when you try to strike back against an oppressive regime?
Nearly always. The trick is in, while doing so, also giving it reason to consider some other way.
In most situations that is a real challenge. Oppression has a way for denying itself alternatives.
Is it better to go about any protest peacefully?
It is always better to go peacefully. It is not always within our emotional, logistical and intellectual means to do so.