Q:

How can we reconcile the supposed contradiction in Genesis 49:5-7 & Malachi 2:4-6?

(KJV)Genesis 49:5-7

Simeon and Levi are brethren; instruments of cruelty are in their habitations. [6] O my soul, come not thou into their secret; unto their assembly, mine honour, be not thou united: for in their anger they slew a man, and in their selfwill they digged down a wall. [7] Cursed be their anger, for it was fierce; and their wrath, for it was cruel: I will divide them in Jacob, and scatter them in Israel.

(KJV)Malachi 2:4-6

And ye shall know that I have sent this commandment unto you, that my covenant might be with Levi, saith the Lord of hosts. [5] My covenant was with him of life and peace; and I gave them to him for the fear wherewith he feared me, and was afraid before my name. [6] The law of truth was in his mouth, and iniquity was not found in his lips: he walked with me in peace and equity, and did turn many away from iniquity.

How can we reconcile the above texts since in Genesis Levi was under a curse but the prophet Malachi seems to allude to Levi as being blessed, could the prophet had been referring to him or his posterity?

A:

Reconciling the two passages is straightforward.
First, by who is speaking:  

Genesis: “Assemble and listen, O sons of Jacob,
      listen to Israel your father. (49:2)
  Malachi:  If you will not listen, if you will not take it to heart to give honor to my name, says the Lord of hosts... (2:2)

In Genesis, Israel is speaking to his sons delivering his final message; in Malachi the LORD of Hosts is speaking. Israel's statements upon his sons does bind the LORD, nor does it negate, alter, or prevent promises the LORD has made to Levi from coming to fruition.
Second, by taking the text for what it says. The OP states "since Levi was under a curse..." Yet the text states Israel cursed their anger not the sons as commentators note [Benson]:

Genesis 49:7. Cursed be their anger — Not their persons. We ought always, in the expressions of our zeal, carefully to distinguish between the sinner and the sin, so as not to love or bless the sin for the sake of the person, nor to hate or curse the person for the sake of the sin.

[Matthew Henry]:

His abhorrence of those brutish lusts that led them to this wickedness: Cursed be their anger. He does not curse their persons, but their lusts.

