Is scope extrusion necessary in the Pi-calculus? What is the real benefit of scope extrusion in the Pi-calculus? I read that it adds more flexiblity to the overly restrictive prior process algebra where the scope of a newly created channel was limited. However, taking a first serious look into Pi-calculus, I came to think that this $\nu$-binder is a source of confusion between channel names and bound variables, which should be considered separately.

There are two binders in pi-calculus. One is a normal binder (just like the one in lambda calculus) in the receive $c(x).Q$ where $x$ is bound in $Q$. However, $(\nu x).P$ is a very strange binder because the scope of $x$ can extend over other parallel processes by an axiom, which is just strange, reminding me of dynamic scoping.

IMHO, this is all due to overloading variables and channel names. If we separate the notion of channel names from variables, we can make the $\nu$-binder a true binder where the variable following $\nu$ is a normal bound variable and we only need to add a reduction rule for it, which is just like the reference cell allocation in ML:
$$ (\nu x)P \longrightarrow P[c/x] $$
where $c$ is a globally fresh channel name. Then, everything made sense to me.

So, what is the benefit of having this strange axiom for scope extrusion when we can simply model it as new channel creation, which to me is much more intuitive and also closer to real implementations.
If we separate the notion of channel names from variables, we can make the ν-binder a true binder where the variable following ν is a normal bound variable and we only need to add a reduction rule for it, which is just like the reference cell allocation in ML:

(νx)P ⟶ P[c/x]

  
  where c is a globally fresh channel name. Then, everything made sense to me.


You are basically correct. 

The reason most people don't do this is that to model your side condition "where $c$ is a globally fresh channel name", you need to give an operational semantics for the $\pi$-calculus which tracks the set of names $\Sigma$ allocated so far. I.e., the rule above would become:

\begin{array}{lcll}  
  \langle\Sigma; \nu x.P\rangle &amp; \to &amp; \langle\Sigma \uplus \{c\}; P[c/x]\rangle &amp; \mbox{where } c \notin \Sigma
\end{array}

Then you'd also need a condition that a configuration is well-formed if the set of names $\Sigma$ is bigger than the free names in $P$, and you'd also need to prove some equivariance/permutation lemmas that configurations and reduction sequences are stable under finite permutations of names. 


You get this all for free from the $\alpha$-equivalence of $\pi$-calculus terms, at the price of introducing the (admittedly somewhat ugly) scope extrusion rule.
However, if you don't like it, you're in good company. Bob Harper does things the way you suggest in his book Practical Foundations for Programming Languages.