There are many Surahs of Quran which have been abrogated with newer ones.
In Surah 2:106:
None of Our revelations do We abrogate or cause to be forgotten, but We substitute something better or similar: Knowest thou not that Allah Hath power over all things?
All the last verses conform to the same standards. Even if abrogation worked the way you seem to believe it does, it wouldn't change the basic principles, at all.
If you want a detailed and in-depth explanation, here:
Refuting lies about Islam: Abrogation in the Quran
It is general perception that Quran is timeless.
''Timeless'' is a very vague description. The
lessons from it apply to all times. The
commands don't. Big difference.
For example, God had Musa (Moses) split a sea to punish a tyrant (Pharoah). Does that mean we should all go around trying to split seas if we hear about tyrants or dictators? Of course not. However, the lesson remains: Tyranny is wrong and so wrong that God may punish Tyrants in severe ways.
Then why would the all-knowing, all-wise, creator and sustainer of the universe; the eternal, self-existent Allah, give such time-bound revelations?
Why would he give ''time-bound revelations''? For the simple reason that different situations have different appropriate responses. Read the third part of my post (
#60 in this thread), which says:
conditions and circumstances: - Generally, in most situations in life (not just religious), the response to one situation is generally different than it would be for another situation. A similar principle applies here. Every command and every such verse has conditions attached to it. It never a blanket statement for all things for eternity. Now, in this chapter (At Tawbah), the circumstances are clearly defined:
''So long, as they are true to you, stand you true to them.'' [9:7]
And if they break their oaths after their treaty and defame your religion, then fight the leaders of disbelief, for indeed, there are no oaths [sacred] to them; [fight them that] they might cease. [9:12]
Would you not fight a people who broke their oaths and determined to expel the Messenger, and they had begun [the attack upon] you the first time? [9:13]
So, it is clear: these verses only apply when they broke their treaties and attacked first.
Let me give you a simple example: A country's leader may order military action against an invading country. But if the dispute is on a smaller scale, he may negotiate with that same country. Does that mean he's contradicting and abrogating and whatnot himself? No, of course not. He's just taking action based on the circumstances.
Why is it so hard to understand that God does the same? He gave commands (that are documented in the Quran) based on the situation of his addressees (the people he was talking to). It's perfectly straightforward and simple.
Moreover, the benign Surahs quoted by most of the muslim scholars and pacifists were revealed during earlier times of Hazrat Muhammad, SAW when he was just starting his public life. As he got control over more and more lands, his revelations also got more and more stricter & virulent.
This facile argument has been thoroughly debunked multiple times.
The article I linked to earlier also deals with most of this argument.
Refuting lies about Islam: Abrogation in the Quran
When the situation called for it, the Muslims were peaceful, adapting means of negotiation and communication to solve problems. When the situation changed, and resolute action was required, they took resolute action. Read the verses you talk about, it is clear and obvious in them.
For example, look at these verses, which come right after the 'verse of the sword' (that is the name given to verse [9:5]):
''So long, as they are true to you, stand you true to them.'' [9:7]
And if they break their oaths after their treaty and defame your religion, then fight the leaders of disbelief, for indeed, there are no oaths [sacred] to them; [fight them that] they might cease. [9:12]
Would you not fight a people who broke their oaths and determined to expel the Messenger, and they had begun [the attack upon] you the first time?
Do you understand what I'm trying to say? Those verses, that command the Muslims to stand true to people who are true to them (in reference to treaties and oaths), are from Surah At-Tawbah, which was one of the last Chapters to be revealed. There is no way any of that could have been abrogated.
Please, stop repeating what you read on anti-Islam or extremist sites. The only ones you're helping by doing that are the Terrorists - the ones I'm trying to combat.
I request you to get out of the tunnel-vision and consider the simple logic I present.