I see your concern, and you're right that we should be careful. But it shouldn't be a problem, as long as you only group together positive terms or negative terms, and not both. To be explicit, here's a statement of a generalisation of the alternating series test that will do the job:
Suppose we have a sequence an, with infinitely many positive and negative terms. Let a 'group' be a maximal collection of consecutive terms of the same sign (let's put 0 with the +'s for definiteness). So the sequence consists of a positive group followed by a negative group followed by a positive group etc. Let the 'value' of a group be the absolute value of the sum of its terms. Then if the sequence of group values is decreasing and tends to zero, the series converges. The alternating series test is the special case where the groups all contain one term.
The proof is essentially the same as for the special case. Let's introduce some more language: let a 'maximum' be a partial sum up to the last term of a positive group, and a 'minimum' be a partial sum up to the last term of a negative group. Now, since the value of any group is smaller than the value of the one that preceded it, the sequence of maxima is decreasing, and each maximum is an upper bound for all subsequent partial sums. Similarly, the minima form an increasing sequence of lower bounds. Finally, since the sequence of values tends to zero, the sequence of maxima and the sequence of minima converge to a common value. Then the series itself must also converge to this value.
In the example you give, where you group 1s and -1s together, these would be split into separate groups and so the values of the group would not tend to zero. OTOH, the original sequence does satisfy the conditions of the test.