I think the answer can come from a fundamental appreciation of the genre of the Talmudic derasha. The purpose was homiletic, to exhort the masses and inspire them, rather than to be a valid kal vachomer.
Your question indeed comes out of the very text of the gemara in Arachin
תניא א"ר אלעזר בן פרטא בוא וראה כמה גדול כח של לשון הרע מנלן ממרגלים ומה המוציא שם רע על עצים ואבנים כך המוציא שם רע על חבירו על אחת כמה וכמה
It is taught in a baraita that Rabbi Elazar ben Perata says: Come and see how great the power of malicious speech is. From where do we derive this? From the punishment received by the spies. And if one who defames the wood and rocks of Eretz Yisrael received such a severe punishment, then with regard to one who defames another person, all the more so will he be punished severely.
If it is indeed an explicit kal vachomer, and a real one, then we would expect the punishment for the chomer to be at least as severe as the kal.
Another example of the kal vachomer in the homiletic genre:
הַלּוֹמֵד מֵחֲבֵרוֹ פֶּרֶק אֶחָד אוֹ הֲלָכָה אַחַת אוֹ פָסוּק אֶחָד אוֹ דִבּוּר אֶחָד אוֹ אֲפִלּוּ אוֹת אַחַת, צָרִיךְ לִנְהוֹג בּוֹ כָבוֹד, שֶׁכֵּן מָצִינוּ בְדָוִד מֶלֶךְ יִשְׂרָאֵל, שֶׁלֹּא לָמַד מֵאֲחִיתֹפֶל אֶלָּא שְׁנֵי דְבָרִים בִּלְבָד, קְרָאוֹ רַבּוֹ אַלּוּפוֹ וּמְיֻדָּעוֹ, שֶׁנֶּאֱמַר (תהלים נה) וְאַתָּה אֱנוֹשׁ כְּעֶרְכִּי אַלּוּפִי וּמְיֻדָּעִי. וַהֲלֹא דְבָרִים קַל וָחֹמֶר, וּמַה דָּוִד מֶלֶךְ יִשְׂרָאֵל, שֶׁלֹּא לָמַד מֵאֲחִיתֹפֶל אֶלָּא שְׁנֵי דְבָרִים בִּלְבַד קְרָאוֹ רַבּוֹ אַלּוּפוֹ וּמְיֻדָּעוֹ, הַלּוֹמֵד מֵחֲבֵרוֹ פֶּרֶק אֶחָד אוֹ הֲלָכָה אַחַת אוֹ פָסוּק אֶחָד אוֹ דִבּוּר אֶחָד אוֹ אֲפִלּוּ אוֹת אַחַת, עַל אַחַת כַּמָּה וְכַמָּה שֶׁצָּרִיךְ לִנְהוֹג בּוֹ כָבוֹד. וְאֵין כָּבוֹד אֶלָּא תוֹרָה, שֶׁנֶּאֱמַר (משלי ג) כָּבוֹד חֲכָמִים יִנְחָלוּ, (משלי כח) וּתְמִימִים יִנְחֲלוּ טוֹב, וְאֵין טוֹב אֶלָּא תוֹרָה, שֶׁנֶּאֱמַר (משלי ד) כִּי לֶקַח טוֹב נָתַתִּי לָכֶם תּוֹרָתִי אַל תַּעֲזֹבוּ:
One who learns from his fellow one chapter, or one halakhah, or one verse, or one word, or even one letter, is obligated to treat him with honor; for so we find with David, king of Israel, who learned from Ahitophel no more than two things, yet called him his master, his guide and his beloved friend, as it is said, “But it was you, a man mine equal, my guide and my beloved friend” (Psalms 55:14). Is this not [an instance of the argument] “from the less to the greater” (kal vehomer)? If David, king of Israel who learned from Ahitophel no more than two things, nevertheless called him his master, his guide and his beloved friend; then in the case of one who learns from his fellow one chapter, or one halakhah, or one verse, or one word, or even one letter, all the more so he is under obligation to treat him with honor. And “honor’” means nothing but Torah, as it is said, “It is honor that sages inherit” (Proverbs 3:35). “And the perfect shall inherit good” (Proverbs 28:10), and “good” means nothing but Torah, as it is said, “For I give you good instruction; do not forsake my Torah” (Proverbs 4:2).
Let me ask you whether this kal vachomer is valid. David learned two halachot from Achitofel. So I can understand the kal vachomer to a chapter. But not to a single halacha, or a verse, or a word, or one letter! The answer is that while employing the structure of kal vachomer, it is not meant to be so solid.
One could proffer other answers, but I would personally swat them away. For example, someone in the comments suggested that it was lashon hara (actually blasphemy) against Hashem. Yes, that is exactly what the gemara in Arachin asks as a question, based on a statement by Rabbi Chanina bar Pappa. If blasphemy, how could you extract the homiletic lesson that it was lashon hara. And they answer by citing another pasuk that shows that it was the lashon hara and not the blasphemy.
One could answer that they deserved a punishment. And other factors transformed it into a very severe punishment. So, the meraglim said lashon hara, but it was part of a larger rebellion. Miriam's actions meanwhile were private, she had various merits, has a brother who Hashem knew would pray for her. What about tzaraat as a punishment for people in general.
One could answer that the death penalty is only imposed after a warning. That is, you need a pasuk for an azhara and a separate pasuk for the onesh. Miriam was the first actor to perform lashon hara in the midbar. Rashi on the transition from Behaalotecha to Shelach says that the juxtaposition is because the meraglim saw Miriam's punishment and did not take heed. That still would not answer why, in general, tzaraat would be the punishment rather than death.
I would return, therefore, to my first answer. Nu, nu, don't look too closely at this homiletic kal vachomer and insist that it work in every respect. Rather, observe a grievous punishment, and take the mussar.