"Waite"

Translation: Call them

[AGreatUserName]

This also means "They should call", the subjunctive of kuita with wa- as the subject prefix.

[Ivoryblossum]

There's a question on another one of the questions in this lesson that touches on what you've said. Is this true for all the words that are prefix-verb root-e? Can they all be either "verb prefix-as-object" or "prefix-as-subject should verb"?

[AGreatUserName]

It depends if the verb NEEDS an object. If it does, it should be clear. Also, some prefixes differ for subjects and objects.

aangalie = s/he should look
mwangalie = look at her/him / you (all) should look

[Phmeza]

In spoken language, is there a tonal difference or is it solely dependent on context?

[AGreatUserName]

There is no tonal difference in the linguistic sense of the word "tone". Swahili is one of very few Bantu languages that has entirely lost tones and that probably occurred due to its very long use as a lingua franca. Languages that are spoken by a significant number of non-native speakers for a long time tend to lose features that are difficult for learners to pick up.

Swahili does of course have intonation (prosody, distinct from the concept of "tone") and that may very well help provide the meaning in certain contexts. Imperative verbs are often spoken more emphatically than other verb forms, so "Walipe!" is probably more likely to mean "Pay them!" and "Walipe," may be more likely "They should pay. / Let them pay." There are always other ways to disambiguate in communication.