No, a downloaded archive can't be installed manually; MacPorts must install it so all the files go in the right places, and so that MacPorts updates its registry to record the fact that all the files have gone in the right places.
I've just tested on my system, and it works fine. Please verify that the tbz2 file that got downloaded on your system has the same size and sha256 hash as on my system:
$ cd /opt/local/var/macports/software/libiconv
$ ls -l libiconv-1.14_0.darwin_10.x86_64.tbz2
-rw-r--r-- 1 macports wheel 1521741 Nov 3 06:47 libiconv-1.14_0.darwin_10.x86_64.tbz2
$ openssl dgst -sha256 libiconv-1.14_0.darwin_10.x86_64.tbz2
SHA256(libiconv-1.14_0.darwin_10.x86_64.tbz2)= d629f4c663d81ff92faca3dad6c2dcecb207ddf33f01f7d4d4f061e288c327cc
$
Also please show me the same information for your bzip2, tar, bsdtar and gnutar commands, to make sure they're sane. Here's what I have on my 10.6.8 system:
$ ls -l {/opt/local,/usr}/bin/{bzip2,{,bsd,gnu}tar}
ls: /opt/local/bin/bsdtar: No such file or directory
ls: /opt/local/bin/tar: No such file or directory
-rwxr-xr-x 1 root wheel 90132 Sep 27 2010 /opt/local/bin/bzip2
-rwxr-xr-x 1 root wheel 905992 Mar 15 2011 /opt/local/bin/gnutar
-rwxr-xr-x 1 root wheel 191920 Jun 24 2010 /usr/bin/bsdtar
-rwxr-xr-x 3 root wheel 121968 Dec 15 2010 /usr/bin/bzip2
-rwxr-xr-x 1 root wheel 991552 Jul 14 2009 /usr/bin/gnutar
lrwxr-xr-x 1 root wheel 6 Nov 8 2009 /usr/bin/tar -> bsdtar
$ openssl dgst -sha256 {/opt/local,/usr}/bin/{bzip2,{,bsd,gnu}tar}
SHA256(/opt/local/bin/bzip2)= 61dc3c6d36208c47a7c8ac19d66a6085c1e767a99d8ea267be417298781245d2
/opt/local/bin/tar: No such file or directory
/opt/local/bin/bsdtar: No such file or directory
SHA256(/opt/local/bin/gnutar)= 27933c35ecc502f5ddc832d871a049d66d3c0b17bb4bff703c748cc16156eafe
SHA256(/usr/bin/bzip2)= 96d00a42f02838bac12d31822417ce35bcd1ab94d615cc9b6632fd76993a3c56
SHA256(/usr/bin/tar)= df10bbc93f9d04f77048e3d3ab6ae3d2085a537a5613c7981db64494a3c9ec76
SHA256(/usr/bin/bsdtar)= df10bbc93f9d04f77048e3d3ab6ae3d2085a537a5613c7981db64494a3c9ec76
SHA256(/usr/bin/gnutar)= b02067331cb0451a8a572907eb49489354fcc13e3563d832005145148fedcb23
$
