Hi Sonali,
It shouldn't be a problem as long as you stick to using only the stereotypes and elements in the FUML spec:
https://www.omg.org/spec/FUML/1.1/PDF for any animation. FUML is a subset of UML that has been given executable semantics by the OMG (I believe that most of FUML is contained by UML4SysML). Moka is an implementation of this standard (though there may be subtle differences as I have not explored this more than a simple demo).
The SysML 1.4 profile for papyrus is provided with OCL constraints where applicable so you should be able to validate the model as correct SysML syntax using just the inbuilt OCL interpreter.
If you need a long term fix for the Architecture Context, you can produce your own architecture contexts for papyrus, there is a section on this in the papyrus manual in the eclipse help documentation (help -> help contents). This is how you can change the tool palettes in diagrams as well as creating new diagram types if needed.