After all, the word in the begining of the pasha upon which the name is based has the definite article attached to it:
זֹאת תִּהְיֶה תּוֹרַת הַמְּצֹרָע, בְּיוֹם טָהֳרָתוֹ: וְהוּבָא, אֶל-הַכֹּהֵן.
We should call it parshat HaMetzora!
People make a similar objection to parshat BaMidbar being called BaMidbar, rather than BeMidbar, since the pasuk has a shva rather than a patach under the bet:
וַיְדַבֵּר יְהוָה אֶל-מֹשֶׁה בְּמִדְבַּר סִינַי, בְּאֹהֶל מוֹעֵד: בְּאֶחָד לַחֹדֶשׁ הַשֵּׁנִי בַּשָּׁנָה הַשֵּׁנִית, לְצֵאתָם מֵאֶרֶץ מִצְרַיִם--לֵאמֹר.
though in the latter example, I actually understand why it could be BaMidbar, as most pronounce it (even though I used the other form for the sefer two posts below). That is, בְּמִדְבַּר סִינַי is a construct form, and the bet gets a shva because we do not use the definite article when in the construct form with a proper noun (Sinai), since the proper noun carries its own definiteness. However, when we cite the name of the sefer we are not using construct form so we make the shva a patach to denote the definiteness.
I do not know why the ה is eliminated from parshat Metzora though.
(perhaps more about elision of ה later)...