O comando
\usepackage[english,greek]{babel}
faz o MikTeX 2.9 rodar para sempre.
SO Windows 7
A saída é
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9)
entering extended mode
(C:/Users/x/AppData/Local/Temp/lyx_tmpdir.Hp3100/lyx_tmpbuf2/negreponti-1.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, afrikaans, ancientgreek, ar
abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan, coptic,
croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, ga
lician, german, greek, gujarati, hindi, hungarian, icelandic, indonesian, inter
lingua, irish, italian, kannada, kurmanji, latin, latvian, lithuanian, malayala
m, marathi, mongolian, mongolianlmc, monogreek, ngerman, nynorsk, oriya, panjab
i, pinyin, polish, portuguese, romanian, russian, sanskrit, serbian, slovak, sl
ovenian, spanish, swedish, swissgerman, tamil, telugu, turkish, turkmen, ukengl
ish, ukrainian, uppersorbian, usenglishmax, welsh, loaded.
Editado:do comentário do OP, código pequeno:
\makeatletter \makeatother
\documentclass[11pt,oneside]{amsart}
\usepackage[iso-8859-7]{inputenc}
\usepackage[a4paper]{geometry}
\usepackage{amsthm}
\usepackage{amstext}
\usepackage{amssymb}
\makeatletter
\usepackage[english,greek]{babel}
%\usepackage[default]{gfsneohellenic}
%\usepackage[LGR,T1]{fontenc} %% LGR encoding is needed for gfsneohellenic
\makeatother
\begin{document} klkk \greektext γφγγ
\end{document}