You should open a case so this can be discussed privately, with your specific details and needs, as any discussion about possibly reducing security on a public forum such as this one greatly increases your risks. Security is sometimes inconvenient but these controls are in place to reduce attack vectors.
If I understand you correctly, you have a SecurID userid with one or two aliases, and the userid matches an AD account that is getting disabled due to lack of use. When the AD account gets disabled, the SecurID userid gets disabled, and that prevents the userid's token from being used with the aliases.
The token belongs to the SecurID userid, and if the userid gets disabled, all the tokens belonging to it can't be used.
Have you tried swapping the userid and alias? That is, assign the token to the AD account (SecurID userid) that the human actually uses regularly, and let the infrequently-used AD accounts be aliases under that SecurID userid. That way, when the AD account gets disabled for not being used, it wouldn't affect the human's SecurID userid.
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