An interesting question, and answer.
It is worrisome to argue with the Gra about the different meanings of words, particularly after the famous (apocryphal?) story of him ordering lashes for the maskil who asserted to him that gila, rina, ditza, chedva, etcetera, were all complete synonyms. But after all, Ibn Ezra said:
ודע כי המלות הם כגופות והטעמים הם כנשמות והגוף לנשמה כמו כלי. ע"כ משפט כל החכמים בכל לשון שישמרו הטעמים ואינם חוששים משנוי המלות אחר שהם שוות בטעמן
And know that the words {lexical items} are like bodies and the meanings are like souls, and the body is as a vessel to the soul. Therefore, the rule of all the scholars of every language is to guard to meanings and not pay particular heed to changes in the words, since they are identical in their meaning.
These might merely be synonyms, then, and the question makes an unwarranted assumption.
But let us grant that assumption. I have another answer in store.
The first cited pasuk actually does speak of rima. That is,
וְלֹא שָׁמְעוּ אֶל מֹשֶׁה וַיּוֹתִרוּ אֲנָשִׁים מִמֶּנּוּ עַד בֹּקֶר וַיָּרֻם תּוֹלָעִים וַיִּבְאַשׁ וַיִּקְצֹף עֲלֵהֶם מֹשֶׁה
Vayarum does not mean that they ascended, but it means that they become wormy. Thus, וַיָּרֻם תּוֹלָעִים means that they became wormy with worms, tolaim. וַיָּרֻם is the verb and תּוֹלָעִים is the noun, functioning as a sort of adverb. This adverb makes even more clear the meaning of the verb.
In the second pasuk, when speaking about the state, there is no verb + adverb. Rather, it wants to refer to a simple noun describing the state (or lack of state). This is called רִמָּה. Maybe, actually, it is an adjective / noun. There was no 'worminess' in it. This is the most efficient and clear way of describing it, given the part-of-speech involved.
As a related aside, ancient science believed in spontaneous generation of worms, such that food rotted and then became wormy, as a development of this rot. Thus, Chazal in the Mechilta claim this is a mikra mesuras, and invert the order of the first pasuk,
וַיָּרֻם תּוֹלָעִים וַיִּבְאַשׁ
They assert that really, of course, the וַיִּבְאַשׁ occurred first. And Ramban has to go out of his way to explain, against Chazal, why in this special instance the developing of worms happened first. See here. The reason I make this aside is to help bolster this understanding of the process, the verbs involved, what rima was ('worming' as opposed to 'rotting', or connected with rotting), and thus why it really would have been inappropriate to say תּוֹלָעִים in the second instance -- it was this developed state of rima, 'worminess', rather than a bunch of worms, which were being discussed.